Starting phenix.real_space_refine on Tue Mar 19 10:28:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/03_2024/6ira_9714_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/03_2024/6ira_9714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/03_2024/6ira_9714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/03_2024/6ira_9714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/03_2024/6ira_9714_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ira_9714/03_2024/6ira_9714_neut.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.018 sd= 1.311 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 15358 2.51 5 N 4040 2.21 5 O 4392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23932 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 5791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 109 Conformer: "B" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 109 bond proxies already assigned to first conformer: 5907 Chain: "A" Number of atoms: 6175 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 6290 Chain: "B" Number of atoms: 5791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 109 Conformer: "B" Number of residues, atoms: 751, 5786 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 723} Chain breaks: 7 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 157 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 109 bond proxies already assigned to first conformer: 5907 Chain: "C" Number of atoms: 6175 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 62 Conformer: "B" Number of residues, atoms: 789, 6170 Classifications: {'peptide': 789} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 756} Chain breaks: 5 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 62 bond proxies already assigned to first conformer: 6290 Time building chain proxies: 24.35, per 1000 atoms: 1.02 Number of scatterers: 23932 At special positions: 0 Unit cell: (111.1, 146.45, 187.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 142 16.00 O 4392 8.00 N 4040 7.00 C 15358 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 320 " distance=2.04 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 456 " distance=2.04 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 320 " distance=2.04 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 456 " distance=2.04 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.74 Conformation dependent library (CDL) restraints added in 7.2 seconds 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 36 sheets defined 43.5% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'D' and resid 45 through 60 Proline residue: D 57 - end of helix removed outlier: 4.296A pdb=" N ALA D 60 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 108 through 120 removed outlier: 3.513A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE D 115 " --> pdb=" O GLN D 111 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 116 " --> pdb=" O MET D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 132 Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.597A pdb=" N TYR D 165 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.877A pdb=" N SER D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 3.765A pdb=" N SER D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 310 removed outlier: 3.812A pdb=" N ARG D 291 " --> pdb=" O SER D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'D' and resid 515 through 522 removed outlier: 3.840A pdb=" N VAL D 521 " --> pdb=" O GLU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 581 Processing helix chain 'D' and resid 602 through 613 removed outlier: 3.811A pdb=" N TRP D 606 " --> pdb=" O GLY D 602 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU D 611 " --> pdb=" O LEU D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 653 removed outlier: 3.693A pdb=" N VAL D 631 " --> pdb=" O SER D 627 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TRP D 634 " --> pdb=" O MET D 630 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA D 635 " --> pdb=" O VAL D 631 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR D 645 " --> pdb=" O PHE D 641 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 649 " --> pdb=" O TYR D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 672 Processing helix chain 'D' and resid 673 through 676 Processing helix chain 'D' and resid 688 through 698 Processing helix chain 'D' and resid 698 through 706 Processing helix chain 'D' and resid 712 through 722 removed outlier: 3.722A pdb=" N ALA D 716 " --> pdb=" O GLY D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 740 removed outlier: 3.654A pdb=" N GLY D 740 " --> pdb=" O ASN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 771 through 785 removed outlier: 3.512A pdb=" N ILE D 775 " --> pdb=" O TRP D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 786 through 796 Processing helix chain 'D' and resid 799 through 803 Processing helix chain 'D' and resid 819 through 836 removed outlier: 3.556A pdb=" N ILE D 836 " --> pdb=" O LEU D 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.772A pdb=" N GLU A 39 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 Processing helix chain 'A' and resid 104 through 113 removed outlier: 4.466A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 removed outlier: 3.927A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.608A pdb=" N SER A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.612A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.693A pdb=" N LEU A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 3.536A pdb=" N ALA A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.552A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 removed outlier: 3.801A pdb=" N ALA A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 4.344A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 559 through 580 Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.558A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 657 removed outlier: 3.850A pdb=" N LEU A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 687 through 696 removed outlier: 3.717A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 707 removed outlier: 3.906A pdb=" N TYR A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG A 704 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.683A pdb=" N ALA A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.558A pdb=" N LYS A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 783 through 792 Processing helix chain 'A' and resid 810 through 844 removed outlier: 3.772A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 60 Proline residue: B 57 - end of helix removed outlier: 4.411A pdb=" N ALA B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.539A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 116 " --> pdb=" O MET B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 132 Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.613A pdb=" N TYR B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.872A pdb=" N SER B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 removed outlier: 3.800A pdb=" N SER B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 310 removed outlier: 3.770A pdb=" N ARG B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 removed outlier: 3.501A pdb=" N ASP B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'B' and resid 515 through 522 removed outlier: 3.618A pdb=" N VAL B 521 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 579 Processing helix chain 'B' and resid 602 through 613 removed outlier: 3.916A pdb=" N TRP B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 653 removed outlier: 3.612A pdb=" N MET B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TRP B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 635 " --> pdb=" O VAL B 631 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 645 " --> pdb=" O PHE B 641 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 649 " --> pdb=" O TYR B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 672 Processing helix chain 'B' and resid 673 through 676 Processing helix chain 'B' and resid 688 through 698 Processing helix chain 'B' and resid 698 through 706 Processing helix chain 'B' and resid 712 through 722 removed outlier: 3.751A pdb=" N ALA B 716 " --> pdb=" O GLY B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 740 removed outlier: 3.613A pdb=" N GLY B 740 " --> pdb=" O ASN B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 785 removed outlier: 3.510A pdb=" N ILE B 775 " --> pdb=" O TRP B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 786 through 796 Processing helix chain 'B' and resid 799 through 803 Processing helix chain 'B' and resid 819 through 837 removed outlier: 3.632A pdb=" N ILE B 836 " --> pdb=" O LEU B 832 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TRP B 837 " --> pdb=" O ILE B 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 52 removed outlier: 3.772A pdb=" N GLU C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 81 Processing helix chain 'C' and resid 104 through 113 removed outlier: 4.466A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.928A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 159 removed outlier: 3.609A pdb=" N SER C 148 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 removed outlier: 3.613A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.693A pdb=" N LEU C 208 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 239 removed outlier: 3.545A pdb=" N ALA C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.552A pdb=" N SER C 255 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 262 removed outlier: 3.801A pdb=" N ALA C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 297 removed outlier: 4.344A pdb=" N HIS C 280 " --> pdb=" O ASN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 328 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 559 through 580 Processing helix chain 'C' and resid 604 through 615 removed outlier: 3.555A pdb=" N LEU C 615 " --> pdb=" O TRP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 657 removed outlier: 3.850A pdb=" N LEU C 655 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 696 removed outlier: 3.716A pdb=" N GLN C 696 " --> pdb=" O TYR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.906A pdb=" N TYR C 703 " --> pdb=" O LEU C 699 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG C 704 " --> pdb=" O SER C 700 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.683A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.558A pdb=" N LYS C 743 " --> pdb=" O GLU C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 769 through 782 Processing helix chain 'C' and resid 783 through 792 Processing helix chain 'C' and resid 810 through 844 removed outlier: 3.773A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 68 through 73 removed outlier: 3.973A pdb=" N GLY D 101 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU D 98 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ILE D 127 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N PHE D 100 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 124 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 199 through 205 removed outlier: 8.542A pdb=" N PHE D 170 " --> pdb=" O ASN D 202 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ILE D 204 " --> pdb=" O PHE D 170 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU D 172 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL D 226 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR D 230 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 229 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 277 through 280 removed outlier: 6.202A pdb=" N VAL D 365 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYS D 374 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 342 through 343 Processing sheet with id=AA5, first strand: chain 'D' and resid 405 through 410 Processing sheet with id=AA6, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AA7, first strand: chain 'D' and resid 523 through 524 Processing sheet with id=AA8, first strand: chain 'D' and resid 682 through 683 removed outlier: 4.298A pdb=" N GLY D 683 " --> pdb=" O ALA D 727 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE D 729 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER D 534 " --> pdb=" O TYR D 730 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 60 through 62 removed outlier: 5.995A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 118 through 120 removed outlier: 6.406A pdb=" N VAL A 118 " --> pdb=" O LEU A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.610A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.241A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 339 through 340 removed outlier: 4.674A pdb=" N GLU A 339 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 478 removed outlier: 5.680A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET A 512 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS A 399 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL A 514 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 401 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU A 517 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY A 757 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 473 through 478 removed outlier: 5.680A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET A 512 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS A 399 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL A 514 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A 401 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA A 515 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY A 759 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU A 517 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY A 757 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 534 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 409 through 412 Processing sheet with id=AB8, first strand: chain 'A' and resid 487 through 490 removed outlier: 4.560A pdb=" N LYS A 495 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 728 through 732 removed outlier: 3.742A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 68 through 73 removed outlier: 3.902A pdb=" N GLY B 97 " --> pdb=" O ASN B 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 37 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY B 101 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B 98 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE B 127 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE B 100 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 124 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 199 through 205 removed outlier: 8.652A pdb=" N PHE B 170 " --> pdb=" O ASN B 202 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ILE B 204 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU B 172 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL B 226 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 230 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 229 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 277 through 280 removed outlier: 6.116A pdb=" N VAL B 365 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS B 374 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 342 through 343 Processing sheet with id=AC5, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.508A pdb=" N ASP B 476 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AC7, first strand: chain 'B' and resid 523 through 524 Processing sheet with id=AC8, first strand: chain 'B' and resid 728 through 731 Processing sheet with id=AC9, first strand: chain 'C' and resid 60 through 62 removed outlier: 5.996A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 118 through 120 removed outlier: 6.406A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 193 through 197 removed outlier: 6.610A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.242A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 339 through 340 removed outlier: 4.674A pdb=" N GLU C 339 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 473 through 478 removed outlier: 5.681A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 473 through 478 removed outlier: 5.681A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N MET C 512 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS C 399 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL C 514 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ALA C 515 " --> pdb=" O GLY C 759 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLY C 759 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU C 517 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY C 757 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 534 " --> pdb=" O PHE C 758 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 409 through 412 Processing sheet with id=AD8, first strand: chain 'C' and resid 487 through 490 removed outlier: 4.560A pdb=" N LYS C 495 " --> pdb=" O VAL C 490 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 728 through 732 removed outlier: 3.742A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.20 Time building geometry restraints manager: 10.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4757 1.33 - 1.45: 6454 1.45 - 1.58: 12983 1.58 - 1.70: 0 1.70 - 1.83: 248 Bond restraints: 24442 Sorted by residual: bond pdb=" C LYS B 628 " pdb=" N ILE B 629 " ideal model delta sigma weight residual 1.333 1.445 -0.112 1.31e-02 5.83e+03 7.28e+01 bond pdb=" C GLY B 753 " pdb=" N TYR B 754 " ideal model delta sigma weight residual 1.331 1.444 -0.114 1.45e-02 4.76e+03 6.16e+01 bond pdb=" C GLY D 753 " pdb=" N TYR D 754 " ideal model delta sigma weight residual 1.331 1.444 -0.114 1.45e-02 4.76e+03 6.15e+01 bond pdb=" C SER D 519 " pdb=" N GLU D 520 " ideal model delta sigma weight residual 1.335 1.233 0.102 1.31e-02 5.83e+03 6.02e+01 bond pdb=" N THR A 230 " pdb=" CA THR A 230 " ideal model delta sigma weight residual 1.459 1.375 0.084 1.20e-02 6.94e+03 4.96e+01 ... (remaining 24437 not shown) Histogram of bond angle deviations from ideal: 94.97 - 104.17: 372 104.17 - 113.38: 14096 113.38 - 122.58: 15157 122.58 - 131.79: 3445 131.79 - 140.99: 62 Bond angle restraints: 33132 Sorted by residual: angle pdb=" CA VAL C 246 " pdb=" C VAL C 246 " pdb=" N TRP C 247 " ideal model delta sigma weight residual 116.16 140.99 -24.83 9.60e-01 1.09e+00 6.69e+02 angle pdb=" CA VAL A 246 " pdb=" C VAL A 246 " pdb=" N TRP A 247 " ideal model delta sigma weight residual 116.16 140.97 -24.81 9.60e-01 1.09e+00 6.68e+02 angle pdb=" O VAL C 246 " pdb=" C VAL C 246 " pdb=" N TRP C 247 " ideal model delta sigma weight residual 122.67 97.69 24.98 1.04e+00 9.25e-01 5.77e+02 angle pdb=" O VAL A 246 " pdb=" C VAL A 246 " pdb=" N TRP A 247 " ideal model delta sigma weight residual 122.67 97.70 24.97 1.04e+00 9.25e-01 5.76e+02 angle pdb=" N PRO B 64 " pdb=" CA PRO B 64 " pdb=" C PRO B 64 " ideal model delta sigma weight residual 113.53 94.97 18.56 1.39e+00 5.18e-01 1.78e+02 ... (remaining 33127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 14030 16.27 - 32.53: 465 32.53 - 48.80: 11 48.80 - 65.06: 4 65.06 - 81.33: 4 Dihedral angle restraints: 14514 sinusoidal: 5578 harmonic: 8936 Sorted by residual: dihedral pdb=" CB CYS D 436 " pdb=" SG CYS D 436 " pdb=" SG CYS D 456 " pdb=" CB CYS D 456 " ideal model delta sinusoidal sigma weight residual -86.00 -167.33 81.33 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS B 436 " pdb=" SG CYS B 436 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual -86.00 -166.79 80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 455 " pdb=" CB CYS A 455 " ideal model delta sinusoidal sigma weight residual -86.00 -164.15 78.15 1 1.00e+01 1.00e-02 7.63e+01 ... (remaining 14511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 3321 0.105 - 0.209: 400 0.209 - 0.314: 49 0.314 - 0.418: 18 0.418 - 0.523: 2 Chirality restraints: 3790 Sorted by residual: chirality pdb=" CA PHE B 636 " pdb=" N PHE B 636 " pdb=" C PHE B 636 " pdb=" CB PHE B 636 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.83e+00 chirality pdb=" CA PHE D 636 " pdb=" N PHE D 636 " pdb=" C PHE D 636 " pdb=" CB PHE D 636 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CA GLU C 210 " pdb=" N GLU C 210 " pdb=" C GLU C 210 " pdb=" CB GLU C 210 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 3787 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 628 " 0.043 2.00e-02 2.50e+03 9.47e-02 8.96e+01 pdb=" C LYS B 628 " -0.163 2.00e-02 2.50e+03 pdb=" O LYS B 628 " 0.069 2.00e-02 2.50e+03 pdb=" N ILE B 629 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 247 " -0.038 2.00e-02 2.50e+03 6.98e-02 4.87e+01 pdb=" C TRP C 247 " 0.121 2.00e-02 2.50e+03 pdb=" O TRP C 247 " -0.043 2.00e-02 2.50e+03 pdb=" N LEU C 248 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 247 " 0.038 2.00e-02 2.50e+03 6.98e-02 4.87e+01 pdb=" C TRP A 247 " -0.121 2.00e-02 2.50e+03 pdb=" O TRP A 247 " 0.043 2.00e-02 2.50e+03 pdb=" N LEU A 248 " 0.040 2.00e-02 2.50e+03 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 20 2.11 - 2.81: 6704 2.81 - 3.51: 32266 3.51 - 4.20: 54312 4.20 - 4.90: 87899 Nonbonded interactions: 181201 Sorted by model distance: nonbonded pdb=" O VAL D 535 " pdb=" N ILE D 750 " model vdw 1.413 2.520 nonbonded pdb=" O VAL B 535 " pdb=" N ILE B 750 " model vdw 1.423 2.520 nonbonded pdb=" OH TYR C 232 " pdb=" CB ALA C 262 " model vdw 1.439 3.460 nonbonded pdb=" O ALA C 228 " pdb=" CB TYR C 232 " model vdw 1.448 2.752 nonbonded pdb=" CG1 VAL B 522 " pdb=" O LEU B 765 " model vdw 1.621 3.460 ... (remaining 181196 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 775 or resid 777 through 844)) selection = (chain 'C' and (resid 25 through 775 or resid 777 through 844)) } ncs_group { reference = (chain 'B' and (resid 34 through 700 or resid 702 through 841)) selection = (chain 'D' and (resid 34 through 700 or resid 702 through 841)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.630 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 82.870 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 24442 Z= 0.573 Angle : 1.419 24.980 33132 Z= 0.909 Chirality : 0.075 0.523 3790 Planarity : 0.008 0.115 4182 Dihedral : 8.452 53.892 8704 Min Nonbonded Distance : 1.413 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.02 % Favored : 89.12 % Rotamer: Outliers : 0.12 % Allowed : 0.16 % Favored : 99.72 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.13), residues: 3028 helix: -2.37 (0.11), residues: 1212 sheet: -0.84 (0.29), residues: 300 loop : -2.64 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.006 TRP C 151 HIS 0.015 0.004 HIS C 134 PHE 0.082 0.005 PHE B 580 TYR 0.052 0.005 TYR D 180 ARG 0.013 0.002 ARG C 839 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1033 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 104 THR cc_start: 0.7161 (p) cc_final: 0.6777 (p) REVERT: D 133 MET cc_start: 0.8117 (mmm) cc_final: 0.7830 (mmm) REVERT: D 150 SER cc_start: 0.8393 (p) cc_final: 0.7162 (t) REVERT: D 199 ASP cc_start: 0.8264 (m-30) cc_final: 0.7904 (p0) REVERT: D 212 ASP cc_start: 0.7877 (m-30) cc_final: 0.7497 (m-30) REVERT: D 248 LEU cc_start: 0.8011 (mt) cc_final: 0.7570 (mt) REVERT: D 267 LEU cc_start: 0.8493 (mt) cc_final: 0.7996 (mt) REVERT: D 453 LYS cc_start: 0.8182 (mttt) cc_final: 0.7941 (tmtt) REVERT: D 473 PHE cc_start: 0.8251 (m-80) cc_final: 0.7461 (m-80) REVERT: D 479 LEU cc_start: 0.8280 (mt) cc_final: 0.7865 (mt) REVERT: D 487 LYS cc_start: 0.6940 (mttt) cc_final: 0.6657 (mmmt) REVERT: D 509 VAL cc_start: 0.7606 (t) cc_final: 0.7145 (t) REVERT: D 562 MET cc_start: 0.9300 (mmm) cc_final: 0.9095 (mtt) REVERT: D 606 TRP cc_start: 0.7324 (m100) cc_final: 0.6966 (m100) REVERT: D 653 MET cc_start: 0.5856 (mmm) cc_final: 0.5564 (mmp) REVERT: D 702 HIS cc_start: 0.9032 (m-70) cc_final: 0.8820 (m-70) REVERT: D 771 TRP cc_start: 0.8227 (m100) cc_final: 0.7806 (m100) REVERT: D 782 PHE cc_start: 0.8922 (m-80) cc_final: 0.8688 (m-80) REVERT: D 783 VAL cc_start: 0.9187 (t) cc_final: 0.8946 (t) REVERT: D 795 TRP cc_start: 0.9273 (m100) cc_final: 0.8762 (m100) REVERT: A 44 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8283 (mp0) REVERT: A 197 PHE cc_start: 0.7739 (m-80) cc_final: 0.7461 (m-80) REVERT: A 354 MET cc_start: 0.8361 (mmm) cc_final: 0.7980 (tpt) REVERT: A 358 ASN cc_start: 0.8841 (m-40) cc_final: 0.8537 (m-40) REVERT: A 472 PHE cc_start: 0.7597 (m-80) cc_final: 0.7326 (m-80) REVERT: A 555 MET cc_start: 0.8463 (mmm) cc_final: 0.8256 (mmp) REVERT: A 563 TRP cc_start: 0.7416 (m100) cc_final: 0.6505 (m100) REVERT: A 611 TRP cc_start: 0.7628 (m100) cc_final: 0.6962 (m100) REVERT: A 639 PHE cc_start: 0.8256 (m-80) cc_final: 0.7680 (m-80) REVERT: A 683 THR cc_start: 0.8743 (p) cc_final: 0.8487 (p) REVERT: A 706 MET cc_start: 0.9437 (mmm) cc_final: 0.9047 (mmm) REVERT: A 707 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8200 (mp0) REVERT: A 752 LEU cc_start: 0.8100 (mt) cc_final: 0.7094 (mm) REVERT: A 786 GLU cc_start: 0.8787 (mt-10) cc_final: 0.7934 (tp30) REVERT: A 789 ASP cc_start: 0.9456 (m-30) cc_final: 0.9235 (t0) REVERT: B 48 GLU cc_start: 0.9221 (mt-10) cc_final: 0.9019 (pm20) REVERT: B 80 LYS cc_start: 0.9033 (mttt) cc_final: 0.8814 (mttp) REVERT: B 102 ASP cc_start: 0.9261 (m-30) cc_final: 0.8989 (t0) REVERT: B 109 VAL cc_start: 0.8056 (t) cc_final: 0.7746 (m) REVERT: B 112 MET cc_start: 0.8398 (mmm) cc_final: 0.8105 (mmm) REVERT: B 122 VAL cc_start: 0.8760 (t) cc_final: 0.8337 (t) REVERT: B 125 LEU cc_start: 0.7769 (mt) cc_final: 0.7127 (mp) REVERT: B 134 ILE cc_start: 0.6640 (mt) cc_final: 0.5720 (mt) REVERT: B 135 MET cc_start: 0.7720 (mmm) cc_final: 0.7222 (mmm) REVERT: B 158 MET cc_start: 0.8838 (mmm) cc_final: 0.7861 (tpt) REVERT: B 159 LEU cc_start: 0.9541 (mt) cc_final: 0.9231 (mm) REVERT: B 161 ILE cc_start: 0.9639 (mt) cc_final: 0.9167 (mt) REVERT: B 169 VAL cc_start: 0.8691 (t) cc_final: 0.8438 (p) REVERT: B 192 ASP cc_start: 0.9344 (m-30) cc_final: 0.9110 (p0) REVERT: B 198 TRP cc_start: 0.7056 (m100) cc_final: 0.6008 (m100) REVERT: B 264 ASN cc_start: 0.9154 (m-40) cc_final: 0.8816 (p0) REVERT: B 267 LEU cc_start: 0.8709 (mt) cc_final: 0.7713 (mp) REVERT: B 334 LEU cc_start: 0.9522 (mt) cc_final: 0.8891 (mm) REVERT: B 338 MET cc_start: 0.8763 (mmm) cc_final: 0.8335 (mmm) REVERT: B 353 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8378 (mp0) REVERT: B 385 LEU cc_start: 0.8780 (mt) cc_final: 0.8320 (mm) REVERT: B 405 HIS cc_start: 0.7812 (m-70) cc_final: 0.7580 (m170) REVERT: B 473 PHE cc_start: 0.8400 (m-80) cc_final: 0.7848 (m-80) REVERT: B 496 MET cc_start: 0.7896 (mmm) cc_final: 0.6658 (mmm) REVERT: B 672 ARG cc_start: 0.9328 (mtt180) cc_final: 0.9034 (mmm160) REVERT: B 700 TYR cc_start: 0.9324 (m-80) cc_final: 0.8885 (p90) REVERT: B 707 LYS cc_start: 0.9441 (mttt) cc_final: 0.9232 (mtmm) REVERT: B 792 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8484 (mt-10) REVERT: B 794 LEU cc_start: 0.8269 (mt) cc_final: 0.7869 (mt) REVERT: B 839 HIS cc_start: 0.7824 (m-70) cc_final: 0.7446 (p-80) REVERT: C 37 LYS cc_start: 0.8945 (mttt) cc_final: 0.8416 (ptpp) REVERT: C 40 GLN cc_start: 0.9426 (mt0) cc_final: 0.9087 (mt0) REVERT: C 44 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8698 (mm-30) REVERT: C 91 LEU cc_start: 0.9156 (mt) cc_final: 0.8830 (mt) REVERT: C 147 GLN cc_start: 0.9331 (mt0) cc_final: 0.8703 (mp10) REVERT: C 166 LEU cc_start: 0.9085 (mt) cc_final: 0.8783 (mt) REVERT: C 172 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8519 (mt-10) REVERT: C 184 LEU cc_start: 0.9689 (mt) cc_final: 0.9468 (mm) REVERT: C 197 PHE cc_start: 0.8442 (m-80) cc_final: 0.7996 (m-80) REVERT: C 219 ILE cc_start: 0.8585 (mt) cc_final: 0.8362 (mp) REVERT: C 324 VAL cc_start: 0.9506 (t) cc_final: 0.9305 (m) REVERT: C 397 ARG cc_start: 0.9132 (mtt180) cc_final: 0.8549 (mmp80) REVERT: C 470 MET cc_start: 0.8467 (mmm) cc_final: 0.7947 (mmm) REVERT: C 517 LEU cc_start: 0.8836 (mt) cc_final: 0.8533 (mt) REVERT: C 639 PHE cc_start: 0.8659 (m-80) cc_final: 0.8182 (m-80) REVERT: C 685 LYS cc_start: 0.9287 (mttt) cc_final: 0.9051 (mtmm) REVERT: C 708 LYS cc_start: 0.9554 (mttt) cc_final: 0.9286 (ptpp) REVERT: C 711 TYR cc_start: 0.8797 (m-80) cc_final: 0.8242 (m-80) REVERT: C 726 LEU cc_start: 0.8699 (mt) cc_final: 0.8363 (mt) REVERT: C 784 PHE cc_start: 0.8593 (m-80) cc_final: 0.8333 (m-10) REVERT: C 790 LYS cc_start: 0.9395 (mttt) cc_final: 0.9122 (pttp) REVERT: C 794 ARG cc_start: 0.7813 (mtt180) cc_final: 0.7556 (tpp-160) outliers start: 3 outliers final: 1 residues processed: 1036 average time/residue: 0.3812 time to fit residues: 588.7673 Evaluate side-chains 654 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 653 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 chunk 239 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 96 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 ASN D 674 HIS D 687 ASN A 38 HIS A 61 ASN A 86 GLN ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS A 171 HIS ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 ASN A 440 ASN A 449 HIS A 520 ASN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS B 85 HIS B 96 HIS ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 HIS B 367 ASN B 444 ASN ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS C 61 ASN ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 161 ASN C 162 HIS ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN C 375 ASN C 405 GLN C 440 ASN C 449 HIS C 521 ASN ** C 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN C 782 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24442 Z= 0.339 Angle : 0.880 16.717 33132 Z= 0.478 Chirality : 0.053 0.376 3790 Planarity : 0.006 0.062 4182 Dihedral : 7.989 37.885 3280 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.26 % Favored : 90.48 % Rotamer: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.86 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.14), residues: 3028 helix: -1.35 (0.13), residues: 1240 sheet: -0.95 (0.28), residues: 312 loop : -2.49 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP D 255 HIS 0.010 0.002 HIS A 162 PHE 0.045 0.003 PHE D 580 TYR 0.070 0.004 TYR C 232 ARG 0.014 0.001 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 785 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 38 VAL cc_start: 0.8647 (t) cc_final: 0.8370 (t) REVERT: D 39 MET cc_start: 0.7646 (mmp) cc_final: 0.7310 (mmp) REVERT: D 80 LYS cc_start: 0.9244 (mttt) cc_final: 0.8821 (mtmt) REVERT: D 120 THR cc_start: 0.8814 (p) cc_final: 0.8576 (p) REVERT: D 152 GLN cc_start: 0.8984 (pm20) cc_final: 0.8761 (pm20) REVERT: D 198 TRP cc_start: 0.7416 (m100) cc_final: 0.6543 (m100) REVERT: D 264 ASN cc_start: 0.9275 (p0) cc_final: 0.8931 (p0) REVERT: D 272 PHE cc_start: 0.9053 (m-80) cc_final: 0.8788 (m-80) REVERT: D 338 MET cc_start: 0.7058 (ptp) cc_final: 0.6514 (ptp) REVERT: D 355 TYR cc_start: 0.8453 (m-80) cc_final: 0.7904 (m-80) REVERT: D 361 LEU cc_start: 0.8373 (mt) cc_final: 0.8149 (mt) REVERT: D 448 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8608 (mp0) REVERT: D 453 LYS cc_start: 0.8395 (mttt) cc_final: 0.8050 (tmtt) REVERT: D 459 PHE cc_start: 0.8202 (m-80) cc_final: 0.7912 (m-80) REVERT: D 473 PHE cc_start: 0.8156 (m-80) cc_final: 0.7448 (m-80) REVERT: D 487 LYS cc_start: 0.7247 (mttt) cc_final: 0.6910 (tppt) REVERT: D 497 ILE cc_start: 0.9303 (mt) cc_final: 0.8838 (tt) REVERT: D 520 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8341 (mt-10) REVERT: D 524 PHE cc_start: 0.6586 (m-80) cc_final: 0.6217 (m-10) REVERT: D 606 TRP cc_start: 0.7523 (m100) cc_final: 0.7188 (m100) REVERT: D 608 LEU cc_start: 0.8986 (mt) cc_final: 0.8743 (mt) REVERT: A 39 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9162 (mp0) REVERT: A 86 GLN cc_start: 0.7546 (mt0) cc_final: 0.7179 (mt0) REVERT: A 113 PHE cc_start: 0.8282 (m-80) cc_final: 0.7978 (m-80) REVERT: A 140 THR cc_start: 0.9417 (p) cc_final: 0.9151 (t) REVERT: A 183 LEU cc_start: 0.8679 (mt) cc_final: 0.8058 (tp) REVERT: A 187 ARG cc_start: 0.8380 (ptp-170) cc_final: 0.8037 (ptp-170) REVERT: A 197 PHE cc_start: 0.7610 (m-80) cc_final: 0.7386 (m-80) REVERT: A 214 LEU cc_start: 0.7739 (mt) cc_final: 0.7477 (mp) REVERT: A 225 GLU cc_start: 0.7677 (tt0) cc_final: 0.7089 (tp30) REVERT: A 245 TYR cc_start: 0.8180 (m-80) cc_final: 0.7326 (m-80) REVERT: A 358 ASN cc_start: 0.9039 (m-40) cc_final: 0.8748 (m-40) REVERT: A 472 PHE cc_start: 0.7891 (m-80) cc_final: 0.7408 (m-80) REVERT: A 477 HIS cc_start: 0.8636 (t-90) cc_final: 0.8296 (t-90) REVERT: A 489 ARG cc_start: 0.6768 (mtt-85) cc_final: 0.6450 (mtt90) REVERT: A 502 MET cc_start: 0.8688 (mtt) cc_final: 0.8338 (mtp) REVERT: A 555 MET cc_start: 0.8374 (mmm) cc_final: 0.7936 (mmp) REVERT: A 611 TRP cc_start: 0.7701 (m100) cc_final: 0.7329 (m100) REVERT: A 639 PHE cc_start: 0.8089 (m-80) cc_final: 0.7658 (m-80) REVERT: A 663 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7878 (ptt-90) REVERT: A 694 ARG cc_start: 0.8750 (mtt180) cc_final: 0.8409 (mtp85) REVERT: A 707 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8232 (mp0) REVERT: A 737 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8186 (mm-30) REVERT: A 786 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8337 (tp30) REVERT: A 789 ASP cc_start: 0.9469 (m-30) cc_final: 0.9205 (t0) REVERT: B 80 LYS cc_start: 0.9128 (mttt) cc_final: 0.8851 (mttp) REVERT: B 100 PHE cc_start: 0.8809 (m-80) cc_final: 0.7629 (m-80) REVERT: B 102 ASP cc_start: 0.9282 (m-30) cc_final: 0.8964 (t0) REVERT: B 134 ILE cc_start: 0.7204 (mt) cc_final: 0.6630 (mm) REVERT: B 135 MET cc_start: 0.7745 (mmm) cc_final: 0.7299 (mmm) REVERT: B 167 TRP cc_start: 0.7635 (m100) cc_final: 0.7135 (m100) REVERT: B 169 VAL cc_start: 0.8622 (t) cc_final: 0.8270 (p) REVERT: B 192 ASP cc_start: 0.9180 (m-30) cc_final: 0.8976 (m-30) REVERT: B 219 LEU cc_start: 0.9754 (mt) cc_final: 0.9474 (pp) REVERT: B 251 TYR cc_start: 0.5106 (m-80) cc_final: 0.4805 (m-80) REVERT: B 334 LEU cc_start: 0.9521 (mt) cc_final: 0.9088 (mm) REVERT: B 338 MET cc_start: 0.8788 (mmm) cc_final: 0.8505 (mmm) REVERT: B 385 LEU cc_start: 0.8945 (mt) cc_final: 0.8702 (mt) REVERT: B 437 ARG cc_start: 0.5493 (mtt180) cc_final: 0.3728 (mtt180) REVERT: B 473 PHE cc_start: 0.8247 (m-80) cc_final: 0.7814 (m-80) REVERT: B 501 VAL cc_start: 0.9152 (t) cc_final: 0.8750 (t) REVERT: B 641 PHE cc_start: 0.7957 (m-80) cc_final: 0.7746 (m-80) REVERT: B 691 GLU cc_start: 0.9245 (mp0) cc_final: 0.8967 (mp0) REVERT: B 696 ASN cc_start: 0.8981 (m-40) cc_final: 0.8720 (m-40) REVERT: B 700 TYR cc_start: 0.9342 (m-80) cc_final: 0.8871 (p90) REVERT: B 781 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8463 (tp-100) REVERT: B 790 GLU cc_start: 0.9419 (tp30) cc_final: 0.9206 (tp30) REVERT: B 792 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8616 (mt-10) REVERT: B 839 HIS cc_start: 0.7922 (m-70) cc_final: 0.7495 (p-80) REVERT: C 39 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8415 (mp0) REVERT: C 44 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8856 (mm-30) REVERT: C 70 ASN cc_start: 0.8952 (p0) cc_final: 0.8418 (p0) REVERT: C 147 GLN cc_start: 0.9415 (mt0) cc_final: 0.8875 (mp10) REVERT: C 166 LEU cc_start: 0.9355 (mt) cc_final: 0.9001 (mt) REVERT: C 172 GLU cc_start: 0.8912 (mt-10) cc_final: 0.7704 (mt-10) REVERT: C 197 PHE cc_start: 0.8062 (m-80) cc_final: 0.7604 (m-80) REVERT: C 207 LEU cc_start: 0.9455 (mt) cc_final: 0.9235 (tt) REVERT: C 240 MET cc_start: 0.3462 (mmt) cc_final: 0.2793 (mmt) REVERT: C 245 TYR cc_start: 0.6859 (m-80) cc_final: 0.6014 (m-10) REVERT: C 281 ILE cc_start: 0.9436 (mt) cc_final: 0.9173 (mt) REVERT: C 303 ASP cc_start: 0.8779 (m-30) cc_final: 0.8403 (t70) REVERT: C 341 ASN cc_start: 0.8314 (m-40) cc_final: 0.8015 (m-40) REVERT: C 361 LEU cc_start: 0.9314 (mt) cc_final: 0.8902 (pt) REVERT: C 434 VAL cc_start: 0.8690 (t) cc_final: 0.8324 (m) REVERT: C 470 MET cc_start: 0.8494 (mmm) cc_final: 0.8027 (mmm) REVERT: C 477 HIS cc_start: 0.8784 (m90) cc_final: 0.8364 (m90) REVERT: C 520 ASN cc_start: 0.8270 (m110) cc_final: 0.7898 (m-40) REVERT: C 538 LEU cc_start: 0.9473 (mt) cc_final: 0.9262 (mt) REVERT: C 576 MET cc_start: 0.8682 (ptt) cc_final: 0.8216 (ptt) REVERT: C 635 VAL cc_start: 0.8936 (t) cc_final: 0.8491 (t) REVERT: C 636 TRP cc_start: 0.8255 (m100) cc_final: 0.8000 (m100) REVERT: C 685 LYS cc_start: 0.9179 (mttt) cc_final: 0.8935 (mtmm) REVERT: C 689 VAL cc_start: 0.9255 (t) cc_final: 0.8912 (p) REVERT: C 694 ARG cc_start: 0.9081 (mtt180) cc_final: 0.8830 (mmt90) REVERT: C 711 TYR cc_start: 0.9057 (m-80) cc_final: 0.8481 (m-80) REVERT: C 712 GLU cc_start: 0.8905 (mp0) cc_final: 0.8705 (mp0) REVERT: C 737 GLU cc_start: 0.9522 (mt-10) cc_final: 0.9110 (tm-30) REVERT: C 760 ILE cc_start: 0.8842 (mt) cc_final: 0.8631 (mm) REVERT: C 786 GLU cc_start: 0.9493 (tp30) cc_final: 0.9091 (tp30) REVERT: C 790 LYS cc_start: 0.9299 (mttt) cc_final: 0.8984 (mmmt) outliers start: 1 outliers final: 0 residues processed: 786 average time/residue: 0.3649 time to fit residues: 438.3634 Evaluate side-chains 601 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 601 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 189 optimal weight: 0.0020 chunk 76 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 300 optimal weight: 0.9980 chunk 247 optimal weight: 9.9990 chunk 276 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 overall best weight: 2.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN D 335 HIS D 697 ASN ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN C 405 GLN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 705 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 24442 Z= 0.224 Angle : 0.738 11.681 33132 Z= 0.395 Chirality : 0.049 0.281 3790 Planarity : 0.005 0.062 4182 Dihedral : 7.108 34.273 3280 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.30 % Favored : 91.44 % Rotamer: Outliers : 0.04 % Allowed : 1.49 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.15), residues: 3028 helix: -0.74 (0.14), residues: 1260 sheet: -0.97 (0.28), residues: 340 loop : -2.29 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP A 636 HIS 0.009 0.001 HIS D 702 PHE 0.036 0.003 PHE C 639 TYR 0.042 0.002 TYR C 232 ARG 0.010 0.001 ARG C 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 720 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 38 VAL cc_start: 0.8645 (t) cc_final: 0.8364 (t) REVERT: D 39 MET cc_start: 0.7482 (mmp) cc_final: 0.7173 (mmp) REVERT: D 80 LYS cc_start: 0.9189 (mttt) cc_final: 0.8783 (mtmt) REVERT: D 133 MET cc_start: 0.8447 (mmm) cc_final: 0.7697 (mpp) REVERT: D 242 GLU cc_start: 0.9535 (tm-30) cc_final: 0.9304 (pp20) REVERT: D 264 ASN cc_start: 0.9252 (p0) cc_final: 0.8902 (p0) REVERT: D 272 PHE cc_start: 0.9090 (m-80) cc_final: 0.8670 (m-80) REVERT: D 334 LEU cc_start: 0.9477 (mm) cc_final: 0.9266 (mm) REVERT: D 355 TYR cc_start: 0.8550 (m-80) cc_final: 0.8155 (m-80) REVERT: D 437 ARG cc_start: 0.5597 (mtt180) cc_final: 0.5386 (mtt180) REVERT: D 448 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8608 (mp0) REVERT: D 487 LYS cc_start: 0.7074 (mttt) cc_final: 0.6441 (mmtt) REVERT: D 497 ILE cc_start: 0.9283 (mt) cc_final: 0.8977 (tt) REVERT: D 499 GLU cc_start: 0.8561 (tp30) cc_final: 0.8308 (tp30) REVERT: D 520 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8433 (mt-10) REVERT: D 524 PHE cc_start: 0.6483 (m-80) cc_final: 0.6138 (m-10) REVERT: D 606 TRP cc_start: 0.7468 (m100) cc_final: 0.6954 (m100) REVERT: D 608 LEU cc_start: 0.8922 (mt) cc_final: 0.8627 (mt) REVERT: D 641 PHE cc_start: 0.8777 (m-80) cc_final: 0.8499 (m-80) REVERT: D 788 MET cc_start: 0.9339 (mtm) cc_final: 0.9016 (mtm) REVERT: D 790 GLU cc_start: 0.9540 (mp0) cc_final: 0.9334 (mp0) REVERT: A 39 GLU cc_start: 0.9346 (mt-10) cc_final: 0.9079 (mp0) REVERT: A 109 TYR cc_start: 0.9095 (m-10) cc_final: 0.8825 (m-10) REVERT: A 140 THR cc_start: 0.9398 (p) cc_final: 0.9094 (t) REVERT: A 183 LEU cc_start: 0.8616 (mt) cc_final: 0.8333 (tp) REVERT: A 214 LEU cc_start: 0.7934 (mt) cc_final: 0.7650 (mp) REVERT: A 477 HIS cc_start: 0.8500 (t-90) cc_final: 0.8274 (t-90) REVERT: A 519 ILE cc_start: 0.9073 (mt) cc_final: 0.8773 (mt) REVERT: A 555 MET cc_start: 0.8057 (mmm) cc_final: 0.7596 (mmp) REVERT: A 577 LEU cc_start: 0.9195 (pp) cc_final: 0.8965 (pp) REVERT: A 611 TRP cc_start: 0.7664 (m100) cc_final: 0.7281 (m100) REVERT: A 663 ARG cc_start: 0.8409 (mtt180) cc_final: 0.7782 (pmt-80) REVERT: A 683 THR cc_start: 0.8449 (p) cc_final: 0.7925 (t) REVERT: A 694 ARG cc_start: 0.8810 (mtt180) cc_final: 0.8488 (mmm-85) REVERT: A 707 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8041 (mp0) REVERT: A 736 LEU cc_start: 0.8178 (tp) cc_final: 0.7826 (tp) REVERT: A 737 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8428 (mm-30) REVERT: A 762 MET cc_start: 0.7606 (mmm) cc_final: 0.7192 (mtp) REVERT: A 786 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8370 (tp30) REVERT: A 789 ASP cc_start: 0.9407 (m-30) cc_final: 0.9140 (t0) REVERT: B 80 LYS cc_start: 0.9105 (mttt) cc_final: 0.8849 (mttp) REVERT: B 99 VAL cc_start: 0.9070 (t) cc_final: 0.8747 (t) REVERT: B 100 PHE cc_start: 0.8869 (m-80) cc_final: 0.7740 (m-80) REVERT: B 102 ASP cc_start: 0.9255 (m-30) cc_final: 0.8901 (t0) REVERT: B 134 ILE cc_start: 0.6810 (mt) cc_final: 0.6287 (mm) REVERT: B 135 MET cc_start: 0.7605 (mmm) cc_final: 0.7200 (mmm) REVERT: B 158 MET cc_start: 0.9391 (mtm) cc_final: 0.8933 (ptp) REVERT: B 159 LEU cc_start: 0.9585 (mm) cc_final: 0.9383 (mm) REVERT: B 167 TRP cc_start: 0.7711 (m100) cc_final: 0.7312 (m100) REVERT: B 182 GLU cc_start: 0.9601 (mt-10) cc_final: 0.9374 (mp0) REVERT: B 334 LEU cc_start: 0.9482 (mt) cc_final: 0.8929 (mm) REVERT: B 338 MET cc_start: 0.8731 (mmm) cc_final: 0.8458 (mmm) REVERT: B 385 LEU cc_start: 0.8857 (mt) cc_final: 0.8631 (mt) REVERT: B 473 PHE cc_start: 0.8215 (m-80) cc_final: 0.7714 (m-80) REVERT: B 496 MET cc_start: 0.8287 (mmm) cc_final: 0.6943 (mmm) REVERT: B 640 ILE cc_start: 0.8792 (mt) cc_final: 0.8581 (mt) REVERT: B 696 ASN cc_start: 0.8953 (m-40) cc_final: 0.8659 (m110) REVERT: B 700 TYR cc_start: 0.9266 (m-80) cc_final: 0.8883 (p90) REVERT: B 705 MET cc_start: 0.9126 (tpp) cc_final: 0.8862 (mmm) REVERT: B 781 GLN cc_start: 0.8700 (tp-100) cc_final: 0.8243 (tp-100) REVERT: B 787 GLU cc_start: 0.9558 (mt-10) cc_final: 0.8999 (mp0) REVERT: B 792 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8701 (mt-10) REVERT: B 794 LEU cc_start: 0.8444 (mt) cc_final: 0.8203 (mt) REVERT: C 39 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8356 (mp0) REVERT: C 44 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8891 (mm-30) REVERT: C 91 LEU cc_start: 0.9059 (mt) cc_final: 0.8836 (mt) REVERT: C 166 LEU cc_start: 0.9282 (mt) cc_final: 0.8832 (mt) REVERT: C 171 HIS cc_start: 0.8757 (t70) cc_final: 0.8356 (t70) REVERT: C 172 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8105 (mt-10) REVERT: C 177 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8423 (tp-100) REVERT: C 197 PHE cc_start: 0.8083 (m-80) cc_final: 0.7761 (m-80) REVERT: C 226 ASP cc_start: 0.8282 (m-30) cc_final: 0.8025 (m-30) REVERT: C 245 TYR cc_start: 0.7718 (m-80) cc_final: 0.7328 (m-10) REVERT: C 303 ASP cc_start: 0.8753 (m-30) cc_final: 0.8346 (t70) REVERT: C 397 ARG cc_start: 0.9266 (mtt180) cc_final: 0.8814 (mmt90) REVERT: C 470 MET cc_start: 0.8402 (mmm) cc_final: 0.7936 (mmm) REVERT: C 501 MET cc_start: 0.9081 (ptp) cc_final: 0.8799 (pmm) REVERT: C 502 MET cc_start: 0.8694 (mpp) cc_final: 0.8310 (mpp) REVERT: C 520 ASN cc_start: 0.8062 (m110) cc_final: 0.7799 (m-40) REVERT: C 538 LEU cc_start: 0.9468 (mt) cc_final: 0.9242 (mt) REVERT: C 539 THR cc_start: 0.9171 (m) cc_final: 0.8690 (p) REVERT: C 576 MET cc_start: 0.8791 (ptt) cc_final: 0.8319 (ptt) REVERT: C 636 TRP cc_start: 0.8151 (m100) cc_final: 0.7873 (m100) REVERT: C 641 MET cc_start: 0.9502 (tmm) cc_final: 0.9159 (ttm) REVERT: C 689 VAL cc_start: 0.9310 (t) cc_final: 0.9019 (p) REVERT: C 690 ASP cc_start: 0.9329 (m-30) cc_final: 0.9006 (m-30) REVERT: C 694 ARG cc_start: 0.9096 (mtt180) cc_final: 0.8873 (mmt90) REVERT: C 712 GLU cc_start: 0.8909 (mp0) cc_final: 0.8563 (mp0) REVERT: C 731 TRP cc_start: 0.9124 (t-100) cc_final: 0.8917 (t-100) REVERT: C 736 LEU cc_start: 0.9101 (mt) cc_final: 0.8819 (mt) REVERT: C 737 GLU cc_start: 0.9455 (mt-10) cc_final: 0.9119 (tm-30) outliers start: 1 outliers final: 0 residues processed: 721 average time/residue: 0.3691 time to fit residues: 414.3304 Evaluate side-chains 599 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 598 time to evaluate : 2.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 186 optimal weight: 9.9990 chunk 279 optimal weight: 3.9990 chunk 295 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 264 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 515 ASN ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 509 GLN A 650 ASN ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 358 ASN C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN ** C 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 HIS C 709 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24442 Z= 0.270 Angle : 0.736 12.086 33132 Z= 0.397 Chirality : 0.048 0.185 3790 Planarity : 0.005 0.064 4182 Dihedral : 6.893 33.980 3280 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.66 % Favored : 90.08 % Rotamer: Outliers : 0.08 % Allowed : 1.73 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.15), residues: 3028 helix: -0.62 (0.14), residues: 1254 sheet: -0.93 (0.28), residues: 318 loop : -2.21 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP A 636 HIS 0.009 0.002 HIS C 67 PHE 0.035 0.003 PHE A 639 TYR 0.043 0.003 TYR C 232 ARG 0.009 0.001 ARG C 755 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 702 time to evaluate : 2.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 38 VAL cc_start: 0.8607 (t) cc_final: 0.8360 (t) REVERT: D 39 MET cc_start: 0.7593 (mmp) cc_final: 0.7276 (mmp) REVERT: D 135 MET cc_start: 0.8791 (mmp) cc_final: 0.8579 (mpp) REVERT: D 142 SER cc_start: 0.8400 (p) cc_final: 0.8186 (p) REVERT: D 152 GLN cc_start: 0.9108 (pm20) cc_final: 0.8056 (pm20) REVERT: D 230 TYR cc_start: 0.8046 (m-80) cc_final: 0.7708 (m-10) REVERT: D 242 GLU cc_start: 0.9484 (tm-30) cc_final: 0.9127 (pp20) REVERT: D 246 LEU cc_start: 0.8655 (mt) cc_final: 0.8273 (mt) REVERT: D 264 ASN cc_start: 0.9316 (p0) cc_final: 0.8887 (p0) REVERT: D 267 LEU cc_start: 0.8833 (mt) cc_final: 0.8575 (mt) REVERT: D 272 PHE cc_start: 0.9237 (m-80) cc_final: 0.8761 (m-80) REVERT: D 338 MET cc_start: 0.7410 (ptp) cc_final: 0.7066 (ptp) REVERT: D 448 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8587 (mp0) REVERT: D 459 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: D 473 PHE cc_start: 0.8230 (m-80) cc_final: 0.7566 (m-80) REVERT: D 497 ILE cc_start: 0.9361 (mt) cc_final: 0.9082 (tt) REVERT: D 499 GLU cc_start: 0.8739 (tp30) cc_final: 0.8392 (tp30) REVERT: D 512 LEU cc_start: 0.7646 (mt) cc_final: 0.7423 (mt) REVERT: D 524 PHE cc_start: 0.6599 (m-80) cc_final: 0.6373 (m-10) REVERT: D 606 TRP cc_start: 0.7589 (m100) cc_final: 0.7091 (m100) REVERT: D 735 LEU cc_start: 0.8837 (mm) cc_final: 0.6813 (mm) REVERT: D 788 MET cc_start: 0.9405 (mtm) cc_final: 0.8933 (mtm) REVERT: D 817 MET cc_start: 0.5244 (tpp) cc_final: 0.4938 (tpp) REVERT: A 39 GLU cc_start: 0.9408 (mt-10) cc_final: 0.9122 (mp0) REVERT: A 140 THR cc_start: 0.9382 (p) cc_final: 0.9006 (t) REVERT: A 183 LEU cc_start: 0.8669 (mt) cc_final: 0.8351 (tp) REVERT: A 214 LEU cc_start: 0.8277 (mt) cc_final: 0.7837 (mt) REVERT: A 225 GLU cc_start: 0.7870 (tt0) cc_final: 0.7251 (tp30) REVERT: A 357 GLN cc_start: 0.8284 (mt0) cc_final: 0.7667 (pp30) REVERT: A 477 HIS cc_start: 0.8529 (t-90) cc_final: 0.8304 (t-90) REVERT: A 519 ILE cc_start: 0.9042 (mt) cc_final: 0.8765 (mt) REVERT: A 533 PHE cc_start: 0.7729 (m-80) cc_final: 0.6968 (m-80) REVERT: A 534 LYS cc_start: 0.8889 (mppt) cc_final: 0.8125 (mtpp) REVERT: A 611 TRP cc_start: 0.7841 (m100) cc_final: 0.7292 (m100) REVERT: A 663 ARG cc_start: 0.8476 (mtt180) cc_final: 0.7849 (pmt-80) REVERT: A 706 MET cc_start: 0.9581 (mmp) cc_final: 0.9367 (mmm) REVERT: A 707 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8415 (mp0) REVERT: A 737 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8484 (mm-30) REVERT: A 786 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8363 (tp30) REVERT: A 789 ASP cc_start: 0.9417 (m-30) cc_final: 0.9214 (t0) REVERT: A 801 ARG cc_start: 0.6479 (mtt180) cc_final: 0.5205 (tpt170) REVERT: B 80 LYS cc_start: 0.9141 (mttt) cc_final: 0.8935 (mttp) REVERT: B 100 PHE cc_start: 0.8975 (m-80) cc_final: 0.8696 (m-80) REVERT: B 102 ASP cc_start: 0.9307 (m-30) cc_final: 0.8854 (t0) REVERT: B 134 ILE cc_start: 0.7045 (mt) cc_final: 0.6469 (mm) REVERT: B 135 MET cc_start: 0.7582 (mmm) cc_final: 0.7259 (mmm) REVERT: B 158 MET cc_start: 0.9431 (mtm) cc_final: 0.9028 (mtt) REVERT: B 167 TRP cc_start: 0.7921 (m100) cc_final: 0.7593 (m100) REVERT: B 251 TYR cc_start: 0.4641 (m-80) cc_final: 0.4139 (m-80) REVERT: B 334 LEU cc_start: 0.9517 (mt) cc_final: 0.8962 (mm) REVERT: B 338 MET cc_start: 0.8799 (mmm) cc_final: 0.8576 (mmm) REVERT: B 355 TYR cc_start: 0.9138 (m-80) cc_final: 0.8888 (m-80) REVERT: B 373 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8215 (mt-10) REVERT: B 385 LEU cc_start: 0.8958 (mt) cc_final: 0.8732 (mt) REVERT: B 437 ARG cc_start: 0.5002 (mtt180) cc_final: 0.2986 (mtt180) REVERT: B 459 PHE cc_start: 0.9114 (m-80) cc_final: 0.8739 (m-80) REVERT: B 473 PHE cc_start: 0.8335 (m-80) cc_final: 0.7870 (m-80) REVERT: B 496 MET cc_start: 0.8444 (mmm) cc_final: 0.7816 (mmm) REVERT: B 507 MET cc_start: 0.9099 (tpp) cc_final: 0.8727 (tpp) REVERT: B 640 ILE cc_start: 0.8777 (mt) cc_final: 0.8562 (mt) REVERT: B 668 LYS cc_start: 0.8996 (mtpt) cc_final: 0.8652 (mmmm) REVERT: B 696 ASN cc_start: 0.8894 (m-40) cc_final: 0.8632 (m-40) REVERT: B 700 TYR cc_start: 0.9303 (m-80) cc_final: 0.8857 (p90) REVERT: B 705 MET cc_start: 0.9023 (tpp) cc_final: 0.8817 (mmm) REVERT: B 773 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7532 (tpt90) REVERT: B 781 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8192 (tp-100) REVERT: B 787 GLU cc_start: 0.9501 (mt-10) cc_final: 0.9043 (mp0) REVERT: B 790 GLU cc_start: 0.9378 (tp30) cc_final: 0.8805 (tp30) REVERT: B 791 LEU cc_start: 0.9226 (mm) cc_final: 0.8963 (mm) REVERT: B 792 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8644 (mt-10) REVERT: B 794 LEU cc_start: 0.8369 (mt) cc_final: 0.7446 (mt) REVERT: C 42 PHE cc_start: 0.9143 (m-80) cc_final: 0.8700 (m-80) REVERT: C 44 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8864 (mm-30) REVERT: C 166 LEU cc_start: 0.9270 (mt) cc_final: 0.8812 (mt) REVERT: C 171 HIS cc_start: 0.9060 (t70) cc_final: 0.8569 (t70) REVERT: C 172 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8171 (mt-10) REVERT: C 181 GLU cc_start: 0.9481 (mt-10) cc_final: 0.9245 (mt-10) REVERT: C 184 LEU cc_start: 0.9591 (mm) cc_final: 0.9301 (mt) REVERT: C 214 LEU cc_start: 0.8638 (mt) cc_final: 0.7925 (mp) REVERT: C 225 GLU cc_start: 0.8625 (pm20) cc_final: 0.8216 (pm20) REVERT: C 226 ASP cc_start: 0.8384 (m-30) cc_final: 0.8165 (m-30) REVERT: C 303 ASP cc_start: 0.8927 (m-30) cc_final: 0.8382 (t0) REVERT: C 306 ARG cc_start: 0.9149 (mtt180) cc_final: 0.8849 (mtt-85) REVERT: C 434 VAL cc_start: 0.8683 (m) cc_final: 0.8381 (t) REVERT: C 470 MET cc_start: 0.8316 (mmm) cc_final: 0.7971 (mmm) REVERT: C 477 HIS cc_start: 0.8965 (m90) cc_final: 0.8486 (m90) REVERT: C 520 ASN cc_start: 0.8156 (m110) cc_final: 0.7768 (m-40) REVERT: C 538 LEU cc_start: 0.9504 (mt) cc_final: 0.9286 (mt) REVERT: C 539 THR cc_start: 0.9375 (m) cc_final: 0.8870 (p) REVERT: C 634 MET cc_start: 0.8717 (ptt) cc_final: 0.8210 (ptp) REVERT: C 635 VAL cc_start: 0.9115 (t) cc_final: 0.8686 (t) REVERT: C 641 MET cc_start: 0.9524 (tmm) cc_final: 0.9290 (ttm) REVERT: C 690 ASP cc_start: 0.9317 (m-30) cc_final: 0.9041 (m-30) REVERT: C 694 ARG cc_start: 0.9168 (mtt180) cc_final: 0.8600 (tpp80) REVERT: C 731 TRP cc_start: 0.9199 (t-100) cc_final: 0.8993 (t-100) REVERT: C 736 LEU cc_start: 0.9069 (mt) cc_final: 0.8827 (mt) outliers start: 1 outliers final: 0 residues processed: 703 average time/residue: 0.3480 time to fit residues: 378.5630 Evaluate side-chains 586 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 585 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.0020 chunk 167 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 252 optimal weight: 8.9990 chunk 204 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 151 optimal weight: 9.9990 chunk 265 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN D 201 GLN ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 515 ASN ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 ASN ** B 697 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24442 Z= 0.256 Angle : 0.740 14.681 33132 Z= 0.395 Chirality : 0.048 0.271 3790 Planarity : 0.005 0.051 4182 Dihedral : 6.707 32.937 3280 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.33 % Favored : 90.41 % Rotamer: Outliers : 0.08 % Allowed : 1.22 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.15), residues: 3028 helix: -0.45 (0.14), residues: 1218 sheet: -1.00 (0.28), residues: 320 loop : -2.13 (0.16), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.003 TRP A 636 HIS 0.015 0.002 HIS D 85 PHE 0.039 0.003 PHE C 639 TYR 0.034 0.002 TYR C 232 ARG 0.015 0.001 ARG A 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 688 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 80 LYS cc_start: 0.9284 (mttt) cc_final: 0.9026 (mtmt) REVERT: D 230 TYR cc_start: 0.8175 (m-80) cc_final: 0.7608 (m-10) REVERT: D 264 ASN cc_start: 0.9363 (p0) cc_final: 0.9053 (p0) REVERT: D 267 LEU cc_start: 0.8887 (mt) cc_final: 0.8615 (mt) REVERT: D 272 PHE cc_start: 0.9264 (m-80) cc_final: 0.8833 (m-80) REVERT: D 338 MET cc_start: 0.7211 (ptp) cc_final: 0.6941 (ptp) REVERT: D 343 TRP cc_start: 0.7343 (t60) cc_final: 0.7094 (t60) REVERT: D 437 ARG cc_start: 0.5376 (mtt180) cc_final: 0.5079 (mtt180) REVERT: D 448 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8541 (mp0) REVERT: D 459 PHE cc_start: 0.7740 (m-10) cc_final: 0.7229 (m-80) REVERT: D 473 PHE cc_start: 0.8315 (m-80) cc_final: 0.7682 (m-80) REVERT: D 497 ILE cc_start: 0.9361 (mt) cc_final: 0.9113 (tt) REVERT: D 499 GLU cc_start: 0.8741 (tp30) cc_final: 0.8343 (tp30) REVERT: D 507 MET cc_start: 0.8578 (tpt) cc_final: 0.8160 (tpt) REVERT: D 512 LEU cc_start: 0.7638 (mt) cc_final: 0.7432 (mt) REVERT: D 515 ASN cc_start: 0.7913 (m110) cc_final: 0.7483 (m-40) REVERT: D 520 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8571 (mt-10) REVERT: D 562 MET cc_start: 0.8735 (mpp) cc_final: 0.8497 (mpp) REVERT: D 606 TRP cc_start: 0.7622 (m100) cc_final: 0.6826 (m100) REVERT: D 608 LEU cc_start: 0.9049 (mt) cc_final: 0.8842 (mt) REVERT: D 788 MET cc_start: 0.9373 (mtm) cc_final: 0.9056 (mtm) REVERT: A 39 GLU cc_start: 0.9426 (mt-10) cc_final: 0.8978 (mp0) REVERT: A 66 THR cc_start: 0.8308 (p) cc_final: 0.8097 (p) REVERT: A 140 THR cc_start: 0.9371 (p) cc_final: 0.9004 (t) REVERT: A 146 HIS cc_start: 0.8989 (m-70) cc_final: 0.8744 (m-70) REVERT: A 166 LEU cc_start: 0.8846 (mt) cc_final: 0.8525 (mt) REVERT: A 183 LEU cc_start: 0.8680 (mt) cc_final: 0.8350 (tp) REVERT: A 225 GLU cc_start: 0.7900 (tt0) cc_final: 0.7264 (tp30) REVERT: A 232 TYR cc_start: 0.8600 (m-80) cc_final: 0.7952 (m-80) REVERT: A 357 GLN cc_start: 0.8293 (mt0) cc_final: 0.7768 (pp30) REVERT: A 358 ASN cc_start: 0.9287 (m-40) cc_final: 0.8599 (m-40) REVERT: A 477 HIS cc_start: 0.8541 (t-90) cc_final: 0.8330 (t-90) REVERT: A 533 PHE cc_start: 0.7496 (m-80) cc_final: 0.6564 (m-80) REVERT: A 534 LYS cc_start: 0.8979 (mppt) cc_final: 0.8132 (mtpp) REVERT: A 611 TRP cc_start: 0.7910 (m100) cc_final: 0.7473 (m100) REVERT: A 647 TYR cc_start: 0.8893 (m-80) cc_final: 0.8640 (m-80) REVERT: A 663 ARG cc_start: 0.8471 (mtt180) cc_final: 0.7982 (pmt-80) REVERT: A 707 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8354 (mp0) REVERT: A 737 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8498 (mm-30) REVERT: A 801 ARG cc_start: 0.6568 (mtt180) cc_final: 0.5205 (tpt170) REVERT: B 80 LYS cc_start: 0.9161 (mttt) cc_final: 0.8939 (mttp) REVERT: B 100 PHE cc_start: 0.9016 (m-80) cc_final: 0.8742 (m-80) REVERT: B 102 ASP cc_start: 0.9247 (m-30) cc_final: 0.8727 (t70) REVERT: B 134 ILE cc_start: 0.7169 (mt) cc_final: 0.6610 (mm) REVERT: B 158 MET cc_start: 0.9448 (mtm) cc_final: 0.9119 (mtp) REVERT: B 167 TRP cc_start: 0.8088 (m100) cc_final: 0.7781 (m100) REVERT: B 200 MET cc_start: 0.8560 (tmm) cc_final: 0.7994 (tmm) REVERT: B 205 THR cc_start: 0.8845 (p) cc_final: 0.8551 (t) REVERT: B 248 LEU cc_start: 0.9245 (mt) cc_final: 0.9044 (mt) REVERT: B 264 ASN cc_start: 0.9186 (m-40) cc_final: 0.8943 (p0) REVERT: B 267 LEU cc_start: 0.8909 (mp) cc_final: 0.7497 (mp) REVERT: B 334 LEU cc_start: 0.9526 (mt) cc_final: 0.8973 (mm) REVERT: B 338 MET cc_start: 0.8777 (mmm) cc_final: 0.8563 (mmm) REVERT: B 347 ASP cc_start: 0.9507 (m-30) cc_final: 0.8419 (p0) REVERT: B 373 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8333 (mt-10) REVERT: B 385 LEU cc_start: 0.9072 (mt) cc_final: 0.8829 (mt) REVERT: B 437 ARG cc_start: 0.5251 (mtt180) cc_final: 0.2988 (ttm110) REVERT: B 473 PHE cc_start: 0.8411 (m-80) cc_final: 0.7946 (m-80) REVERT: B 478 TYR cc_start: 0.8238 (m-10) cc_final: 0.7215 (m-10) REVERT: B 496 MET cc_start: 0.8545 (mmm) cc_final: 0.8114 (mmm) REVERT: B 504 ARG cc_start: 0.9121 (mtt180) cc_final: 0.8439 (mpt-90) REVERT: B 507 MET cc_start: 0.9091 (tpp) cc_final: 0.8673 (tpp) REVERT: B 640 ILE cc_start: 0.8826 (mt) cc_final: 0.8594 (mt) REVERT: B 668 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8786 (tppp) REVERT: B 696 ASN cc_start: 0.8896 (m-40) cc_final: 0.8604 (m-40) REVERT: B 700 TYR cc_start: 0.9271 (m-80) cc_final: 0.8871 (p90) REVERT: B 705 MET cc_start: 0.9064 (tpp) cc_final: 0.8827 (mmm) REVERT: B 773 ARG cc_start: 0.8290 (mmm160) cc_final: 0.7575 (tpt170) REVERT: B 781 GLN cc_start: 0.8644 (tp-100) cc_final: 0.8274 (tp-100) REVERT: B 783 VAL cc_start: 0.9219 (m) cc_final: 0.8928 (m) REVERT: B 787 GLU cc_start: 0.9497 (mt-10) cc_final: 0.9087 (mp0) REVERT: B 790 GLU cc_start: 0.9209 (tp30) cc_final: 0.8608 (tp30) REVERT: B 792 GLU cc_start: 0.9383 (mt-10) cc_final: 0.8889 (mt-10) REVERT: B 794 LEU cc_start: 0.8466 (mt) cc_final: 0.7664 (mt) REVERT: B 824 LEU cc_start: 0.7867 (mt) cc_final: 0.7608 (tp) REVERT: C 37 LYS cc_start: 0.9187 (ptpp) cc_final: 0.8987 (ptmm) REVERT: C 42 PHE cc_start: 0.9135 (m-80) cc_final: 0.8610 (m-80) REVERT: C 44 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8937 (mm-30) REVERT: C 147 GLN cc_start: 0.9498 (mt0) cc_final: 0.9229 (mt0) REVERT: C 166 LEU cc_start: 0.9272 (mt) cc_final: 0.8712 (mt) REVERT: C 171 HIS cc_start: 0.9106 (t70) cc_final: 0.8615 (t70) REVERT: C 184 LEU cc_start: 0.9587 (mm) cc_final: 0.9199 (mt) REVERT: C 214 LEU cc_start: 0.8597 (mt) cc_final: 0.8191 (mp) REVERT: C 226 ASP cc_start: 0.8531 (m-30) cc_final: 0.8243 (m-30) REVERT: C 303 ASP cc_start: 0.8953 (m-30) cc_final: 0.8431 (t0) REVERT: C 306 ARG cc_start: 0.9166 (mtt180) cc_final: 0.8861 (mtt-85) REVERT: C 316 LYS cc_start: 0.9568 (tptp) cc_final: 0.9266 (tppt) REVERT: C 390 ARG cc_start: 0.8628 (mtt180) cc_final: 0.8382 (ttm170) REVERT: C 397 ARG cc_start: 0.9438 (mtt180) cc_final: 0.9015 (ttm110) REVERT: C 470 MET cc_start: 0.8223 (mmm) cc_final: 0.7894 (mmm) REVERT: C 477 HIS cc_start: 0.8909 (m90) cc_final: 0.8569 (m90) REVERT: C 501 MET cc_start: 0.9099 (ptp) cc_final: 0.8814 (pmm) REVERT: C 502 MET cc_start: 0.8775 (mpp) cc_final: 0.8444 (mpp) REVERT: C 520 ASN cc_start: 0.8395 (m110) cc_final: 0.8192 (m110) REVERT: C 539 THR cc_start: 0.9332 (m) cc_final: 0.8858 (p) REVERT: C 641 MET cc_start: 0.9541 (tmm) cc_final: 0.9273 (ttm) REVERT: C 694 ARG cc_start: 0.9165 (mtt180) cc_final: 0.8647 (tpp80) REVERT: C 736 LEU cc_start: 0.9041 (mt) cc_final: 0.8753 (mt) outliers start: 1 outliers final: 0 residues processed: 689 average time/residue: 0.3480 time to fit residues: 371.5980 Evaluate side-chains 561 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 561 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 296 optimal weight: 1.9990 chunk 245 optimal weight: 0.0020 chunk 137 optimal weight: 0.0010 chunk 24 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 155 optimal weight: 30.0000 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 697 ASN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.7135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24442 Z= 0.200 Angle : 0.695 13.758 33132 Z= 0.368 Chirality : 0.048 0.266 3790 Planarity : 0.004 0.050 4182 Dihedral : 6.352 32.404 3280 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.66 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.15), residues: 3028 helix: -0.25 (0.14), residues: 1222 sheet: -0.96 (0.28), residues: 318 loop : -2.04 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP A 636 HIS 0.009 0.001 HIS A 780 PHE 0.047 0.002 PHE C 639 TYR 0.026 0.002 TYR C 232 ARG 0.016 0.001 ARG C 673 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 690 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 38 VAL cc_start: 0.8769 (t) cc_final: 0.8493 (t) REVERT: D 183 PHE cc_start: 0.8617 (m-80) cc_final: 0.8015 (m-80) REVERT: D 230 TYR cc_start: 0.8130 (m-80) cc_final: 0.7370 (m-10) REVERT: D 264 ASN cc_start: 0.9400 (p0) cc_final: 0.9092 (p0) REVERT: D 267 LEU cc_start: 0.8874 (mt) cc_final: 0.8592 (mt) REVERT: D 272 PHE cc_start: 0.9274 (m-80) cc_final: 0.8837 (m-80) REVERT: D 343 TRP cc_start: 0.7257 (t60) cc_final: 0.6909 (t60) REVERT: D 437 ARG cc_start: 0.5511 (mtt180) cc_final: 0.5228 (mtt180) REVERT: D 459 PHE cc_start: 0.7603 (m-10) cc_final: 0.6979 (m-80) REVERT: D 473 PHE cc_start: 0.8210 (m-80) cc_final: 0.7631 (m-80) REVERT: D 496 MET cc_start: 0.8437 (mmt) cc_final: 0.8015 (mmm) REVERT: D 497 ILE cc_start: 0.9354 (mt) cc_final: 0.9097 (tt) REVERT: D 499 GLU cc_start: 0.8714 (tp30) cc_final: 0.8398 (tp30) REVERT: D 507 MET cc_start: 0.8435 (tpt) cc_final: 0.8141 (tpt) REVERT: D 520 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8560 (mt-10) REVERT: D 606 TRP cc_start: 0.7397 (m100) cc_final: 0.7130 (m100) REVERT: D 608 LEU cc_start: 0.9019 (mt) cc_final: 0.8815 (mt) REVERT: D 788 MET cc_start: 0.9268 (mtm) cc_final: 0.8866 (mtm) REVERT: A 39 GLU cc_start: 0.9426 (mt-10) cc_final: 0.8967 (mp0) REVERT: A 66 THR cc_start: 0.8287 (p) cc_final: 0.8026 (p) REVERT: A 128 TYR cc_start: 0.8319 (m-10) cc_final: 0.7966 (m-80) REVERT: A 131 LYS cc_start: 0.8835 (mptt) cc_final: 0.7946 (tmmt) REVERT: A 140 THR cc_start: 0.9331 (p) cc_final: 0.8973 (t) REVERT: A 183 LEU cc_start: 0.8737 (mt) cc_final: 0.8423 (tp) REVERT: A 225 GLU cc_start: 0.7871 (tt0) cc_final: 0.7271 (tp30) REVERT: A 232 TYR cc_start: 0.8677 (m-80) cc_final: 0.8110 (m-80) REVERT: A 345 ASP cc_start: 0.8915 (m-30) cc_final: 0.8630 (t0) REVERT: A 357 GLN cc_start: 0.8305 (mt0) cc_final: 0.7785 (pp30) REVERT: A 358 ASN cc_start: 0.9289 (m-40) cc_final: 0.8465 (m110) REVERT: A 477 HIS cc_start: 0.8556 (t-90) cc_final: 0.8345 (t-90) REVERT: A 489 ARG cc_start: 0.5818 (mmt90) cc_final: 0.4992 (tpp-160) REVERT: A 533 PHE cc_start: 0.7362 (m-80) cc_final: 0.6503 (m-80) REVERT: A 534 LYS cc_start: 0.8912 (mppt) cc_final: 0.8290 (ptmt) REVERT: A 611 TRP cc_start: 0.8016 (m100) cc_final: 0.7576 (m100) REVERT: A 663 ARG cc_start: 0.8559 (mtt180) cc_final: 0.8079 (pmt-80) REVERT: A 737 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8547 (mm-30) REVERT: B 80 LYS cc_start: 0.9120 (mttt) cc_final: 0.8724 (ptpp) REVERT: B 102 ASP cc_start: 0.9216 (m-30) cc_final: 0.8760 (t70) REVERT: B 133 MET cc_start: 0.9361 (mmp) cc_final: 0.9123 (mmm) REVERT: B 134 ILE cc_start: 0.7168 (mt) cc_final: 0.6818 (mm) REVERT: B 158 MET cc_start: 0.9382 (mtm) cc_final: 0.9130 (mtp) REVERT: B 167 TRP cc_start: 0.8068 (m100) cc_final: 0.7808 (m100) REVERT: B 169 VAL cc_start: 0.8808 (t) cc_final: 0.8594 (p) REVERT: B 200 MET cc_start: 0.8604 (tmm) cc_final: 0.8159 (tmm) REVERT: B 205 THR cc_start: 0.8842 (p) cc_final: 0.8506 (t) REVERT: B 235 GLU cc_start: 0.8708 (tt0) cc_final: 0.8379 (tt0) REVERT: B 251 TYR cc_start: 0.5061 (m-80) cc_final: 0.3988 (m-80) REVERT: B 264 ASN cc_start: 0.9249 (m-40) cc_final: 0.8880 (p0) REVERT: B 267 LEU cc_start: 0.8906 (mp) cc_final: 0.7454 (mp) REVERT: B 293 ARG cc_start: 0.9513 (mtt180) cc_final: 0.9238 (mmm-85) REVERT: B 334 LEU cc_start: 0.9505 (mt) cc_final: 0.8944 (mm) REVERT: B 338 MET cc_start: 0.8791 (mmm) cc_final: 0.8572 (mmm) REVERT: B 373 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8249 (mt-10) REVERT: B 459 PHE cc_start: 0.8768 (m-80) cc_final: 0.8237 (m-80) REVERT: B 473 PHE cc_start: 0.8327 (m-80) cc_final: 0.7847 (m-80) REVERT: B 496 MET cc_start: 0.8490 (mmm) cc_final: 0.7485 (mmm) REVERT: B 504 ARG cc_start: 0.9068 (mtt180) cc_final: 0.8311 (mpt-90) REVERT: B 507 MET cc_start: 0.9052 (tpp) cc_final: 0.8610 (tpp) REVERT: B 562 MET cc_start: 0.9529 (mmp) cc_final: 0.9230 (tpp) REVERT: B 653 MET cc_start: 0.8126 (mtm) cc_final: 0.7408 (tpt) REVERT: B 668 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8773 (tppp) REVERT: B 696 ASN cc_start: 0.8858 (m-40) cc_final: 0.8525 (m110) REVERT: B 700 TYR cc_start: 0.9256 (m-80) cc_final: 0.8855 (p90) REVERT: B 777 LEU cc_start: 0.8957 (tp) cc_final: 0.8735 (mm) REVERT: B 781 GLN cc_start: 0.8534 (tp-100) cc_final: 0.8177 (tp-100) REVERT: B 787 GLU cc_start: 0.9448 (mt-10) cc_final: 0.8991 (mp0) REVERT: B 790 GLU cc_start: 0.9176 (tp30) cc_final: 0.8621 (tp30) REVERT: B 791 LEU cc_start: 0.9376 (mt) cc_final: 0.9084 (mt) REVERT: B 792 GLU cc_start: 0.9373 (mt-10) cc_final: 0.8906 (mt-10) REVERT: B 794 LEU cc_start: 0.8520 (mt) cc_final: 0.7669 (mt) REVERT: B 824 LEU cc_start: 0.7835 (mt) cc_final: 0.7544 (tp) REVERT: C 37 LYS cc_start: 0.9173 (ptpp) cc_final: 0.8955 (ptmm) REVERT: C 70 ASN cc_start: 0.9157 (p0) cc_final: 0.8943 (p0) REVERT: C 74 MET cc_start: 0.7802 (mpp) cc_final: 0.7247 (mpp) REVERT: C 138 LEU cc_start: 0.9214 (mt) cc_final: 0.8493 (pt) REVERT: C 147 GLN cc_start: 0.9482 (mt0) cc_final: 0.9176 (mt0) REVERT: C 166 LEU cc_start: 0.9224 (mt) cc_final: 0.8710 (mt) REVERT: C 171 HIS cc_start: 0.9058 (t70) cc_final: 0.8276 (t70) REVERT: C 184 LEU cc_start: 0.9581 (mm) cc_final: 0.9363 (mt) REVERT: C 214 LEU cc_start: 0.8662 (mt) cc_final: 0.8107 (mp) REVERT: C 226 ASP cc_start: 0.8545 (m-30) cc_final: 0.8278 (m-30) REVERT: C 303 ASP cc_start: 0.8917 (m-30) cc_final: 0.8366 (t0) REVERT: C 306 ARG cc_start: 0.9176 (mtt180) cc_final: 0.8937 (mtt-85) REVERT: C 316 LYS cc_start: 0.9539 (tptp) cc_final: 0.9229 (tppt) REVERT: C 378 LYS cc_start: 0.8639 (mttt) cc_final: 0.8374 (tptp) REVERT: C 390 ARG cc_start: 0.8646 (mtt180) cc_final: 0.8391 (ttm170) REVERT: C 397 ARG cc_start: 0.9423 (mtt180) cc_final: 0.9037 (mmt90) REVERT: C 470 MET cc_start: 0.8159 (mmm) cc_final: 0.7919 (mmm) REVERT: C 477 HIS cc_start: 0.8903 (m90) cc_final: 0.8551 (m90) REVERT: C 501 MET cc_start: 0.9077 (ptp) cc_final: 0.8792 (pmm) REVERT: C 502 MET cc_start: 0.8800 (mpp) cc_final: 0.8404 (mpp) REVERT: C 539 THR cc_start: 0.9378 (m) cc_final: 0.8970 (p) REVERT: C 607 MET cc_start: 0.8974 (tmm) cc_final: 0.8654 (tmm) REVERT: C 634 MET cc_start: 0.8512 (ptt) cc_final: 0.8242 (ptt) REVERT: C 641 MET cc_start: 0.9528 (tmm) cc_final: 0.9251 (ttm) REVERT: C 690 ASP cc_start: 0.9277 (m-30) cc_final: 0.9043 (m-30) REVERT: C 694 ARG cc_start: 0.9110 (mtt180) cc_final: 0.8821 (ttm-80) REVERT: C 696 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8682 (tm-30) REVERT: C 736 LEU cc_start: 0.9054 (mt) cc_final: 0.8752 (mt) REVERT: C 786 GLU cc_start: 0.9597 (tp30) cc_final: 0.9091 (tp30) REVERT: C 790 LYS cc_start: 0.9312 (mmmt) cc_final: 0.8876 (mmmt) outliers start: 0 outliers final: 0 residues processed: 690 average time/residue: 0.3700 time to fit residues: 404.2925 Evaluate side-chains 569 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 569 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 0.0050 chunk 33 optimal weight: 9.9990 chunk 168 optimal weight: 7.9990 chunk 216 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 249 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 294 optimal weight: 4.9990 chunk 184 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS D 503 GLN D 515 ASN ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 766 GLN ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 GLN ** C 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 24442 Z= 0.249 Angle : 0.723 14.874 33132 Z= 0.383 Chirality : 0.048 0.284 3790 Planarity : 0.004 0.050 4182 Dihedral : 6.289 31.846 3280 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 21.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.46 % Favored : 90.28 % Rotamer: Outliers : 0.04 % Allowed : 0.94 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.15), residues: 3028 helix: -0.27 (0.14), residues: 1234 sheet: -1.08 (0.28), residues: 328 loop : -1.95 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP A 636 HIS 0.012 0.002 HIS A 780 PHE 0.032 0.002 PHE D 183 TYR 0.026 0.002 TYR D 180 ARG 0.010 0.001 ARG C 673 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 671 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 133 MET cc_start: 0.8878 (mmm) cc_final: 0.8068 (mpp) REVERT: D 152 GLN cc_start: 0.9094 (mm110) cc_final: 0.8724 (mm110) REVERT: D 158 MET cc_start: 0.9634 (ptp) cc_final: 0.9260 (ptp) REVERT: D 198 TRP cc_start: 0.7266 (m100) cc_final: 0.6825 (m100) REVERT: D 220 LYS cc_start: 0.8502 (ptpp) cc_final: 0.8186 (ptpt) REVERT: D 230 TYR cc_start: 0.7932 (m-80) cc_final: 0.7667 (m-10) REVERT: D 272 PHE cc_start: 0.9323 (m-80) cc_final: 0.8731 (m-80) REVERT: D 338 MET cc_start: 0.7426 (ptp) cc_final: 0.7030 (ptp) REVERT: D 343 TRP cc_start: 0.7245 (t60) cc_final: 0.6832 (t60) REVERT: D 361 LEU cc_start: 0.9128 (mt) cc_final: 0.8896 (mt) REVERT: D 437 ARG cc_start: 0.5700 (mtt180) cc_final: 0.5362 (mtt180) REVERT: D 459 PHE cc_start: 0.7642 (m-10) cc_final: 0.7092 (m-80) REVERT: D 473 PHE cc_start: 0.8362 (m-80) cc_final: 0.7814 (m-80) REVERT: D 496 MET cc_start: 0.8590 (mmt) cc_final: 0.8126 (mmm) REVERT: D 497 ILE cc_start: 0.9393 (mt) cc_final: 0.9182 (tt) REVERT: D 499 GLU cc_start: 0.8796 (tp30) cc_final: 0.8447 (tp30) REVERT: D 520 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8607 (mt-10) REVERT: D 606 TRP cc_start: 0.7616 (m100) cc_final: 0.7312 (m100) REVERT: D 608 LEU cc_start: 0.9086 (mt) cc_final: 0.8880 (mt) REVERT: D 668 LYS cc_start: 0.9400 (mttt) cc_final: 0.9148 (tppt) REVERT: D 788 MET cc_start: 0.9289 (mtm) cc_final: 0.8922 (mtm) REVERT: A 39 GLU cc_start: 0.9448 (mt-10) cc_final: 0.8984 (mp0) REVERT: A 66 THR cc_start: 0.8283 (p) cc_final: 0.8041 (p) REVERT: A 140 THR cc_start: 0.9352 (p) cc_final: 0.9021 (t) REVERT: A 183 LEU cc_start: 0.8756 (mt) cc_final: 0.8426 (tp) REVERT: A 207 LEU cc_start: 0.9412 (mt) cc_final: 0.9203 (mt) REVERT: A 225 GLU cc_start: 0.7885 (tt0) cc_final: 0.7264 (tp30) REVERT: A 232 TYR cc_start: 0.8758 (m-80) cc_final: 0.8294 (m-80) REVERT: A 245 TYR cc_start: 0.8480 (m-80) cc_final: 0.7596 (m-80) REVERT: A 345 ASP cc_start: 0.8912 (m-30) cc_final: 0.8647 (t70) REVERT: A 357 GLN cc_start: 0.8310 (mt0) cc_final: 0.7778 (pp30) REVERT: A 358 ASN cc_start: 0.9330 (m-40) cc_final: 0.8363 (m110) REVERT: A 477 HIS cc_start: 0.8548 (t-90) cc_final: 0.8316 (t-90) REVERT: A 611 TRP cc_start: 0.8063 (m100) cc_final: 0.7551 (m100) REVERT: A 663 ARG cc_start: 0.8594 (mtt180) cc_final: 0.8158 (pmt-80) REVERT: A 737 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8586 (mm-30) REVERT: B 80 LYS cc_start: 0.9164 (mttt) cc_final: 0.8749 (ptpp) REVERT: B 102 ASP cc_start: 0.9264 (m-30) cc_final: 0.8709 (t70) REVERT: B 134 ILE cc_start: 0.7517 (mt) cc_final: 0.7216 (mm) REVERT: B 135 MET cc_start: 0.7909 (mmp) cc_final: 0.7559 (mmp) REVERT: B 158 MET cc_start: 0.9403 (mtm) cc_final: 0.9184 (mtp) REVERT: B 167 TRP cc_start: 0.8133 (m100) cc_final: 0.7829 (m100) REVERT: B 200 MET cc_start: 0.8689 (tmm) cc_final: 0.8117 (tmm) REVERT: B 235 GLU cc_start: 0.8764 (tt0) cc_final: 0.8506 (tt0) REVERT: B 251 TYR cc_start: 0.4905 (m-80) cc_final: 0.4069 (m-80) REVERT: B 264 ASN cc_start: 0.9284 (m-40) cc_final: 0.8897 (p0) REVERT: B 267 LEU cc_start: 0.8918 (mp) cc_final: 0.7459 (mp) REVERT: B 293 ARG cc_start: 0.9518 (mtt180) cc_final: 0.9221 (mmm-85) REVERT: B 334 LEU cc_start: 0.9540 (mt) cc_final: 0.9001 (mm) REVERT: B 338 MET cc_start: 0.8787 (mmm) cc_final: 0.8582 (mmm) REVERT: B 373 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8199 (mt-10) REVERT: B 385 LEU cc_start: 0.8834 (mm) cc_final: 0.8463 (mt) REVERT: B 455 CYS cc_start: 0.7096 (m) cc_final: 0.5982 (m) REVERT: B 456 CYS cc_start: 0.8838 (m) cc_final: 0.8605 (p) REVERT: B 473 PHE cc_start: 0.8423 (m-80) cc_final: 0.7963 (m-80) REVERT: B 499 GLU cc_start: 0.9216 (tp30) cc_final: 0.8891 (tp30) REVERT: B 504 ARG cc_start: 0.9103 (mtt180) cc_final: 0.8464 (mpt-90) REVERT: B 507 MET cc_start: 0.9097 (tpp) cc_final: 0.8799 (tpp) REVERT: B 562 MET cc_start: 0.9662 (mmp) cc_final: 0.9302 (tpp) REVERT: B 696 ASN cc_start: 0.8729 (m-40) cc_final: 0.8375 (m110) REVERT: B 700 TYR cc_start: 0.9262 (m-80) cc_final: 0.8838 (p90) REVERT: B 781 GLN cc_start: 0.8596 (tp-100) cc_final: 0.8293 (tp-100) REVERT: B 787 GLU cc_start: 0.9438 (mt-10) cc_final: 0.8899 (mp0) REVERT: B 790 GLU cc_start: 0.9176 (tp30) cc_final: 0.8702 (tp30) REVERT: B 792 GLU cc_start: 0.9377 (mt-10) cc_final: 0.8928 (mt-10) REVERT: B 794 LEU cc_start: 0.8589 (mt) cc_final: 0.7818 (mt) REVERT: C 37 LYS cc_start: 0.9195 (ptpp) cc_final: 0.8970 (ptmm) REVERT: C 147 GLN cc_start: 0.9483 (mt0) cc_final: 0.9162 (mt0) REVERT: C 166 LEU cc_start: 0.9258 (mt) cc_final: 0.8734 (mt) REVERT: C 171 HIS cc_start: 0.8849 (t70) cc_final: 0.8329 (t70) REVERT: C 184 LEU cc_start: 0.9581 (mm) cc_final: 0.9374 (mt) REVERT: C 214 LEU cc_start: 0.8753 (mt) cc_final: 0.8200 (mp) REVERT: C 226 ASP cc_start: 0.8561 (m-30) cc_final: 0.8265 (m-30) REVERT: C 303 ASP cc_start: 0.9014 (m-30) cc_final: 0.8415 (t0) REVERT: C 306 ARG cc_start: 0.9125 (mtt180) cc_final: 0.8803 (mtt-85) REVERT: C 316 LYS cc_start: 0.9537 (tptp) cc_final: 0.9252 (tppt) REVERT: C 378 LYS cc_start: 0.8662 (mttt) cc_final: 0.8407 (tptp) REVERT: C 390 ARG cc_start: 0.8751 (mtt180) cc_final: 0.8135 (ptt-90) REVERT: C 397 ARG cc_start: 0.9492 (mtt180) cc_final: 0.9040 (ttm-80) REVERT: C 470 MET cc_start: 0.8147 (mmm) cc_final: 0.7922 (mmm) REVERT: C 477 HIS cc_start: 0.8942 (m90) cc_final: 0.8588 (m90) REVERT: C 501 MET cc_start: 0.9133 (ptp) cc_final: 0.8775 (pmm) REVERT: C 502 MET cc_start: 0.8807 (mpp) cc_final: 0.8407 (mpp) REVERT: C 536 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8497 (tp-100) REVERT: C 539 THR cc_start: 0.9450 (m) cc_final: 0.9063 (p) REVERT: C 607 MET cc_start: 0.9046 (tmm) cc_final: 0.8843 (tmm) REVERT: C 634 MET cc_start: 0.8551 (ptt) cc_final: 0.8233 (ptt) REVERT: C 635 VAL cc_start: 0.9092 (t) cc_final: 0.8683 (t) REVERT: C 639 PHE cc_start: 0.8782 (m-80) cc_final: 0.8518 (m-80) REVERT: C 641 MET cc_start: 0.9486 (tmm) cc_final: 0.9210 (ttm) REVERT: C 690 ASP cc_start: 0.9257 (m-30) cc_final: 0.9015 (m-30) REVERT: C 694 ARG cc_start: 0.9116 (mtt180) cc_final: 0.8841 (ttm-80) REVERT: C 736 LEU cc_start: 0.9034 (mt) cc_final: 0.8703 (mt) REVERT: C 786 GLU cc_start: 0.9625 (tp30) cc_final: 0.9079 (tp30) REVERT: C 790 LYS cc_start: 0.9305 (mmmt) cc_final: 0.8742 (mmmt) outliers start: 1 outliers final: 1 residues processed: 672 average time/residue: 0.3361 time to fit residues: 353.8382 Evaluate side-chains 537 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 536 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 57 optimal weight: 50.0000 chunk 187 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 231 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN D 515 ASN ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 499 ASN ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 687 ASN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN C 650 ASN ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.7886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24442 Z= 0.235 Angle : 0.742 15.144 33132 Z= 0.393 Chirality : 0.049 0.233 3790 Planarity : 0.004 0.047 4182 Dihedral : 6.280 31.130 3280 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.42 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.15), residues: 3028 helix: -0.27 (0.14), residues: 1230 sheet: -1.15 (0.28), residues: 332 loop : -1.96 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP A 636 HIS 0.010 0.002 HIS C 780 PHE 0.035 0.002 PHE A 639 TYR 0.033 0.002 TYR D 180 ARG 0.009 0.001 ARG C 673 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 672 time to evaluate : 2.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 133 MET cc_start: 0.9051 (mmm) cc_final: 0.8282 (mpp) REVERT: D 152 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8697 (mm110) REVERT: D 220 LYS cc_start: 0.8504 (ptpp) cc_final: 0.8206 (ptpt) REVERT: D 230 TYR cc_start: 0.7981 (m-80) cc_final: 0.7774 (m-80) REVERT: D 272 PHE cc_start: 0.9242 (m-80) cc_final: 0.8499 (m-80) REVERT: D 338 MET cc_start: 0.7480 (ptp) cc_final: 0.7178 (ptp) REVERT: D 343 TRP cc_start: 0.7337 (t60) cc_final: 0.6852 (t60) REVERT: D 437 ARG cc_start: 0.5452 (mtt180) cc_final: 0.5214 (mtt180) REVERT: D 459 PHE cc_start: 0.7678 (m-10) cc_final: 0.7166 (m-80) REVERT: D 473 PHE cc_start: 0.8425 (m-80) cc_final: 0.7925 (m-80) REVERT: D 497 ILE cc_start: 0.9448 (mt) cc_final: 0.9152 (tt) REVERT: D 499 GLU cc_start: 0.8797 (tp30) cc_final: 0.8371 (tp30) REVERT: D 504 ARG cc_start: 0.8904 (mtt180) cc_final: 0.8677 (mpt-90) REVERT: D 507 MET cc_start: 0.8421 (tpt) cc_final: 0.8180 (tpp) REVERT: D 518 ARG cc_start: 0.8923 (mtt-85) cc_final: 0.8537 (mmt90) REVERT: D 562 MET cc_start: 0.8781 (mpp) cc_final: 0.8389 (mpp) REVERT: D 606 TRP cc_start: 0.7615 (m100) cc_final: 0.7306 (m100) REVERT: D 608 LEU cc_start: 0.9090 (mt) cc_final: 0.8880 (mt) REVERT: D 774 GLN cc_start: 0.9371 (mp10) cc_final: 0.8845 (mp10) REVERT: D 788 MET cc_start: 0.9148 (mtm) cc_final: 0.8935 (mtm) REVERT: A 39 GLU cc_start: 0.9461 (mt-10) cc_final: 0.8987 (mp0) REVERT: A 66 THR cc_start: 0.8288 (p) cc_final: 0.8034 (p) REVERT: A 121 LEU cc_start: 0.8566 (mt) cc_final: 0.8331 (mt) REVERT: A 131 LYS cc_start: 0.9050 (mptt) cc_final: 0.8078 (tmmt) REVERT: A 140 THR cc_start: 0.9342 (p) cc_final: 0.8994 (t) REVERT: A 172 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7183 (mp0) REVERT: A 183 LEU cc_start: 0.8797 (mt) cc_final: 0.8563 (tp) REVERT: A 225 GLU cc_start: 0.7893 (tt0) cc_final: 0.7257 (tp30) REVERT: A 232 TYR cc_start: 0.8814 (m-80) cc_final: 0.8341 (m-80) REVERT: A 245 TYR cc_start: 0.8509 (m-80) cc_final: 0.8132 (m-10) REVERT: A 345 ASP cc_start: 0.8939 (m-30) cc_final: 0.8485 (t0) REVERT: A 358 ASN cc_start: 0.9384 (m-40) cc_final: 0.9081 (m110) REVERT: A 433 LYS cc_start: 0.7450 (tmtt) cc_final: 0.7197 (tptp) REVERT: A 477 HIS cc_start: 0.8544 (t-90) cc_final: 0.8307 (t-90) REVERT: A 533 PHE cc_start: 0.7579 (m-80) cc_final: 0.7356 (m-80) REVERT: A 539 THR cc_start: 0.8960 (p) cc_final: 0.8532 (p) REVERT: A 611 TRP cc_start: 0.8105 (m100) cc_final: 0.7617 (m100) REVERT: A 663 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8316 (ppt170) REVERT: A 736 LEU cc_start: 0.8561 (tp) cc_final: 0.7944 (tp) REVERT: A 737 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8643 (mm-30) REVERT: A 762 MET cc_start: 0.8109 (mmm) cc_final: 0.7842 (mmm) REVERT: B 80 LYS cc_start: 0.9142 (mttt) cc_final: 0.8840 (ptpp) REVERT: B 100 PHE cc_start: 0.9245 (m-80) cc_final: 0.8999 (m-80) REVERT: B 102 ASP cc_start: 0.9164 (m-30) cc_final: 0.8762 (t0) REVERT: B 134 ILE cc_start: 0.7638 (mt) cc_final: 0.7234 (mm) REVERT: B 135 MET cc_start: 0.8048 (mmp) cc_final: 0.7668 (mmp) REVERT: B 167 TRP cc_start: 0.8163 (m100) cc_final: 0.7870 (m100) REVERT: B 200 MET cc_start: 0.8704 (tmm) cc_final: 0.8054 (tmm) REVERT: B 235 GLU cc_start: 0.8775 (tt0) cc_final: 0.8512 (tt0) REVERT: B 264 ASN cc_start: 0.9293 (m-40) cc_final: 0.8950 (p0) REVERT: B 267 LEU cc_start: 0.8968 (mp) cc_final: 0.7585 (mp) REVERT: B 293 ARG cc_start: 0.9482 (mtt180) cc_final: 0.9195 (mmm-85) REVERT: B 334 LEU cc_start: 0.9527 (mt) cc_final: 0.8996 (mm) REVERT: B 355 TYR cc_start: 0.9405 (m-80) cc_final: 0.8980 (m-80) REVERT: B 385 LEU cc_start: 0.8789 (mm) cc_final: 0.8421 (mt) REVERT: B 473 PHE cc_start: 0.8447 (m-80) cc_final: 0.7977 (m-80) REVERT: B 496 MET cc_start: 0.8391 (mmm) cc_final: 0.7545 (mmm) REVERT: B 499 GLU cc_start: 0.9224 (tp30) cc_final: 0.8910 (tp30) REVERT: B 504 ARG cc_start: 0.9080 (mtt180) cc_final: 0.8448 (mpt-90) REVERT: B 507 MET cc_start: 0.9082 (tpp) cc_final: 0.8847 (tpp) REVERT: B 562 MET cc_start: 0.9631 (mmp) cc_final: 0.9260 (tpp) REVERT: B 670 PHE cc_start: 0.9138 (m-80) cc_final: 0.8899 (m-80) REVERT: B 672 ARG cc_start: 0.9182 (mtt180) cc_final: 0.8929 (mmm160) REVERT: B 696 ASN cc_start: 0.8722 (m-40) cc_final: 0.8371 (m110) REVERT: B 700 TYR cc_start: 0.9271 (m-80) cc_final: 0.8839 (p90) REVERT: B 781 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8162 (tp-100) REVERT: B 785 ASP cc_start: 0.6711 (m-30) cc_final: 0.5857 (m-30) REVERT: B 787 GLU cc_start: 0.9415 (mt-10) cc_final: 0.8891 (mp0) REVERT: B 790 GLU cc_start: 0.9143 (tp30) cc_final: 0.8608 (tp30) REVERT: B 791 LEU cc_start: 0.9426 (mt) cc_final: 0.9213 (mt) REVERT: B 792 GLU cc_start: 0.9354 (mt-10) cc_final: 0.8881 (mt-10) REVERT: B 794 LEU cc_start: 0.8627 (mt) cc_final: 0.7855 (mt) REVERT: C 147 GLN cc_start: 0.9475 (mt0) cc_final: 0.9179 (mt0) REVERT: C 166 LEU cc_start: 0.9243 (mt) cc_final: 0.8787 (mt) REVERT: C 171 HIS cc_start: 0.8719 (t-90) cc_final: 0.8237 (t70) REVERT: C 177 GLN cc_start: 0.8921 (tp40) cc_final: 0.8697 (tp-100) REVERT: C 181 GLU cc_start: 0.9461 (mt-10) cc_final: 0.9224 (mt-10) REVERT: C 184 LEU cc_start: 0.9578 (mm) cc_final: 0.9243 (tp) REVERT: C 214 LEU cc_start: 0.8761 (mt) cc_final: 0.8303 (mp) REVERT: C 303 ASP cc_start: 0.9053 (m-30) cc_final: 0.8445 (t0) REVERT: C 306 ARG cc_start: 0.9143 (mtt180) cc_final: 0.8797 (mtt-85) REVERT: C 316 LYS cc_start: 0.9526 (tptp) cc_final: 0.9237 (tppt) REVERT: C 378 LYS cc_start: 0.8709 (mttt) cc_final: 0.8465 (tptp) REVERT: C 390 ARG cc_start: 0.8812 (mtt180) cc_final: 0.8185 (ptt-90) REVERT: C 397 ARG cc_start: 0.9537 (mtt180) cc_final: 0.9100 (ttm110) REVERT: C 477 HIS cc_start: 0.8961 (m90) cc_final: 0.8598 (m90) REVERT: C 501 MET cc_start: 0.9126 (ptp) cc_final: 0.8648 (pmm) REVERT: C 502 MET cc_start: 0.8829 (mpp) cc_final: 0.8356 (mpp) REVERT: C 536 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8394 (tp40) REVERT: C 539 THR cc_start: 0.9452 (m) cc_final: 0.9081 (p) REVERT: C 573 VAL cc_start: 0.9061 (t) cc_final: 0.8605 (t) REVERT: C 634 MET cc_start: 0.8550 (ptt) cc_final: 0.8186 (ptt) REVERT: C 635 VAL cc_start: 0.9094 (t) cc_final: 0.8519 (t) REVERT: C 639 PHE cc_start: 0.8750 (m-80) cc_final: 0.8526 (m-80) REVERT: C 641 MET cc_start: 0.9478 (tmm) cc_final: 0.9112 (ttt) REVERT: C 736 LEU cc_start: 0.9065 (mt) cc_final: 0.8761 (mt) outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.3379 time to fit residues: 355.4237 Evaluate side-chains 536 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 536 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 20.0000 chunk 257 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 273 optimal weight: 6.9990 chunk 180 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 515 ASN ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 HIS ** A 727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 ASN B 687 ASN ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.8365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24442 Z= 0.271 Angle : 0.772 15.903 33132 Z= 0.409 Chirality : 0.050 0.281 3790 Planarity : 0.004 0.045 4182 Dihedral : 6.393 31.531 3280 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.95 % Favored : 89.78 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.15), residues: 3028 helix: -0.30 (0.14), residues: 1218 sheet: -1.25 (0.28), residues: 322 loop : -2.01 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.004 TRP C 636 HIS 0.018 0.002 HIS C 780 PHE 0.030 0.002 PHE A 639 TYR 0.035 0.002 TYR D 180 ARG 0.008 0.001 ARG C 673 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 654 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 133 MET cc_start: 0.9077 (mmm) cc_final: 0.8397 (mpp) REVERT: D 152 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8931 (mm110) REVERT: D 198 TRP cc_start: 0.7385 (m100) cc_final: 0.7115 (m100) REVERT: D 220 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8334 (ptpt) REVERT: D 338 MET cc_start: 0.7510 (ptp) cc_final: 0.7220 (ptp) REVERT: D 378 TRP cc_start: 0.7797 (m100) cc_final: 0.7570 (t-100) REVERT: D 459 PHE cc_start: 0.7649 (m-10) cc_final: 0.7277 (m-80) REVERT: D 473 PHE cc_start: 0.8505 (m-80) cc_final: 0.7995 (m-80) REVERT: D 499 GLU cc_start: 0.8887 (tp30) cc_final: 0.8410 (tp30) REVERT: D 507 MET cc_start: 0.8640 (tpt) cc_final: 0.8359 (tpp) REVERT: D 520 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8754 (mt-10) REVERT: D 562 MET cc_start: 0.8822 (mpp) cc_final: 0.8588 (mpp) REVERT: D 606 TRP cc_start: 0.7577 (m100) cc_final: 0.7052 (m100) REVERT: D 608 LEU cc_start: 0.9053 (mt) cc_final: 0.8846 (mt) REVERT: D 788 MET cc_start: 0.9197 (mtm) cc_final: 0.8847 (mtm) REVERT: D 792 GLU cc_start: 0.9352 (tm-30) cc_final: 0.9076 (tm-30) REVERT: A 39 GLU cc_start: 0.9485 (mt-10) cc_final: 0.9038 (mp0) REVERT: A 66 THR cc_start: 0.8362 (p) cc_final: 0.8122 (p) REVERT: A 131 LYS cc_start: 0.9105 (mptt) cc_final: 0.8110 (tmmt) REVERT: A 140 THR cc_start: 0.9293 (p) cc_final: 0.8940 (t) REVERT: A 146 HIS cc_start: 0.9203 (m-70) cc_final: 0.8780 (m-70) REVERT: A 225 GLU cc_start: 0.7856 (tt0) cc_final: 0.7434 (pm20) REVERT: A 232 TYR cc_start: 0.8944 (m-80) cc_final: 0.8555 (m-80) REVERT: A 245 TYR cc_start: 0.8451 (m-80) cc_final: 0.7602 (m-80) REVERT: A 345 ASP cc_start: 0.9002 (m-30) cc_final: 0.8699 (t0) REVERT: A 358 ASN cc_start: 0.9505 (m-40) cc_final: 0.9253 (m110) REVERT: A 456 TYR cc_start: 0.5562 (m-80) cc_final: 0.5326 (m-80) REVERT: A 477 HIS cc_start: 0.8568 (t-90) cc_final: 0.8297 (t-90) REVERT: A 533 PHE cc_start: 0.7698 (m-80) cc_final: 0.7398 (m-80) REVERT: A 539 THR cc_start: 0.9004 (p) cc_final: 0.8596 (p) REVERT: A 611 TRP cc_start: 0.8144 (m100) cc_final: 0.7649 (m100) REVERT: A 663 ARG cc_start: 0.8550 (mtt180) cc_final: 0.8256 (ptt-90) REVERT: A 698 GLU cc_start: 0.9378 (tm-30) cc_final: 0.9156 (tm-30) REVERT: A 736 LEU cc_start: 0.8677 (tp) cc_final: 0.8055 (tp) REVERT: A 737 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8687 (mm-30) REVERT: B 80 LYS cc_start: 0.9139 (mttt) cc_final: 0.8845 (ptpp) REVERT: B 100 PHE cc_start: 0.9265 (m-80) cc_final: 0.8960 (m-80) REVERT: B 102 ASP cc_start: 0.9132 (m-30) cc_final: 0.8897 (t70) REVERT: B 134 ILE cc_start: 0.7883 (mt) cc_final: 0.7490 (mm) REVERT: B 135 MET cc_start: 0.8102 (mmp) cc_final: 0.7786 (mmp) REVERT: B 167 TRP cc_start: 0.8224 (m100) cc_final: 0.7463 (m100) REVERT: B 235 GLU cc_start: 0.8852 (tt0) cc_final: 0.8501 (tt0) REVERT: B 264 ASN cc_start: 0.9369 (m-40) cc_final: 0.8961 (p0) REVERT: B 267 LEU cc_start: 0.8992 (mp) cc_final: 0.7581 (mp) REVERT: B 293 ARG cc_start: 0.9485 (mtt180) cc_final: 0.9188 (mmm-85) REVERT: B 334 LEU cc_start: 0.9475 (mt) cc_final: 0.9239 (mm) REVERT: B 338 MET cc_start: 0.8555 (mmp) cc_final: 0.8143 (mmm) REVERT: B 373 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7868 (mp0) REVERT: B 385 LEU cc_start: 0.8874 (mm) cc_final: 0.8578 (mm) REVERT: B 473 PHE cc_start: 0.8546 (m-80) cc_final: 0.8129 (m-80) REVERT: B 496 MET cc_start: 0.8596 (mmm) cc_final: 0.7811 (mmm) REVERT: B 499 GLU cc_start: 0.9212 (tp30) cc_final: 0.8878 (tp30) REVERT: B 504 ARG cc_start: 0.9087 (mtt180) cc_final: 0.8445 (mmt90) REVERT: B 507 MET cc_start: 0.8983 (tpp) cc_final: 0.8629 (tpp) REVERT: B 668 LYS cc_start: 0.8628 (tppp) cc_final: 0.8381 (mmmm) REVERT: B 696 ASN cc_start: 0.8725 (m-40) cc_final: 0.8348 (m110) REVERT: B 705 MET cc_start: 0.9085 (tpp) cc_final: 0.8868 (mmm) REVERT: B 781 GLN cc_start: 0.8603 (tp-100) cc_final: 0.8207 (tp-100) REVERT: B 785 ASP cc_start: 0.6658 (m-30) cc_final: 0.5706 (m-30) REVERT: B 787 GLU cc_start: 0.9427 (mt-10) cc_final: 0.8973 (mp0) REVERT: B 790 GLU cc_start: 0.9147 (tp30) cc_final: 0.8590 (tp30) REVERT: B 792 GLU cc_start: 0.9345 (mt-10) cc_final: 0.8879 (mt-10) REVERT: B 794 LEU cc_start: 0.8740 (mt) cc_final: 0.8026 (mt) REVERT: C 37 LYS cc_start: 0.9260 (ptpp) cc_final: 0.9022 (ptmm) REVERT: C 127 ILE cc_start: 0.9506 (mt) cc_final: 0.9219 (tp) REVERT: C 147 GLN cc_start: 0.9434 (mt0) cc_final: 0.9174 (mt0) REVERT: C 166 LEU cc_start: 0.9269 (mt) cc_final: 0.8791 (mt) REVERT: C 171 HIS cc_start: 0.8733 (t-90) cc_final: 0.8056 (t-90) REVERT: C 177 GLN cc_start: 0.8916 (tp40) cc_final: 0.8650 (tp-100) REVERT: C 181 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9218 (mt-10) REVERT: C 184 LEU cc_start: 0.9589 (mm) cc_final: 0.9263 (tp) REVERT: C 303 ASP cc_start: 0.9154 (m-30) cc_final: 0.8503 (t0) REVERT: C 306 ARG cc_start: 0.9190 (mtt180) cc_final: 0.8795 (mtt-85) REVERT: C 316 LYS cc_start: 0.9542 (tptp) cc_final: 0.9196 (tppt) REVERT: C 378 LYS cc_start: 0.8797 (mttt) cc_final: 0.8512 (tptp) REVERT: C 390 ARG cc_start: 0.8922 (mtt180) cc_final: 0.8273 (ptt-90) REVERT: C 397 ARG cc_start: 0.9584 (mtt180) cc_final: 0.9172 (ttm-80) REVERT: C 400 ILE cc_start: 0.7861 (mt) cc_final: 0.7534 (mt) REVERT: C 477 HIS cc_start: 0.9033 (m90) cc_final: 0.8588 (m90) REVERT: C 501 MET cc_start: 0.9168 (ptp) cc_final: 0.8712 (pmm) REVERT: C 502 MET cc_start: 0.8890 (mpp) cc_final: 0.8339 (mpp) REVERT: C 513 ILE cc_start: 0.8356 (mt) cc_final: 0.8068 (mt) REVERT: C 536 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8276 (tp40) REVERT: C 539 THR cc_start: 0.9441 (m) cc_final: 0.9190 (p) REVERT: C 607 MET cc_start: 0.9222 (tmm) cc_final: 0.9013 (tmm) REVERT: C 634 MET cc_start: 0.8508 (ptt) cc_final: 0.7903 (ptp) REVERT: C 641 MET cc_start: 0.9445 (tmm) cc_final: 0.9160 (ttm) REVERT: C 736 LEU cc_start: 0.9064 (mt) cc_final: 0.8807 (mt) outliers start: 0 outliers final: 0 residues processed: 654 average time/residue: 0.3374 time to fit residues: 350.5846 Evaluate side-chains 537 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 304 optimal weight: 7.9990 chunk 280 optimal weight: 0.9980 chunk 242 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN D 515 ASN ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN C 405 GLN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN C 650 ASN ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.8573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24442 Z= 0.197 Angle : 0.734 15.831 33132 Z= 0.384 Chirality : 0.049 0.261 3790 Planarity : 0.004 0.049 4182 Dihedral : 6.130 30.931 3280 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.27 % Favored : 91.47 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.15), residues: 3028 helix: -0.18 (0.14), residues: 1238 sheet: -1.16 (0.28), residues: 324 loop : -1.88 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP A 636 HIS 0.016 0.001 HIS C 780 PHE 0.037 0.002 PHE C 639 TYR 0.031 0.002 TYR D 502 ARG 0.008 0.001 ARG A 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6056 Ramachandran restraints generated. 3028 Oldfield, 0 Emsley, 3028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 659 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 133 MET cc_start: 0.9077 (mmm) cc_final: 0.8436 (mpp) REVERT: D 152 GLN cc_start: 0.9280 (mm-40) cc_final: 0.8976 (mm110) REVERT: D 158 MET cc_start: 0.9601 (ptp) cc_final: 0.9362 (ptp) REVERT: D 198 TRP cc_start: 0.7282 (m100) cc_final: 0.7053 (m100) REVERT: D 264 ASN cc_start: 0.9437 (p0) cc_final: 0.9111 (p0) REVERT: D 267 LEU cc_start: 0.9004 (mt) cc_final: 0.8708 (mt) REVERT: D 334 LEU cc_start: 0.9373 (mm) cc_final: 0.9160 (mm) REVERT: D 338 MET cc_start: 0.7676 (ptp) cc_final: 0.7213 (ptp) REVERT: D 459 PHE cc_start: 0.7614 (m-10) cc_final: 0.7200 (m-10) REVERT: D 473 PHE cc_start: 0.8382 (m-80) cc_final: 0.7833 (m-80) REVERT: D 507 MET cc_start: 0.8718 (tpt) cc_final: 0.8129 (tpt) REVERT: D 518 ARG cc_start: 0.9070 (mtt-85) cc_final: 0.8800 (mmt90) REVERT: D 520 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8684 (mt-10) REVERT: D 562 MET cc_start: 0.8766 (mpp) cc_final: 0.8534 (mpp) REVERT: D 606 TRP cc_start: 0.7271 (m100) cc_final: 0.6908 (m100) REVERT: D 608 LEU cc_start: 0.9039 (mt) cc_final: 0.8837 (mt) REVERT: D 703 GLN cc_start: 0.9648 (tp-100) cc_final: 0.9372 (tm-30) REVERT: D 735 LEU cc_start: 0.8768 (mm) cc_final: 0.8460 (mm) REVERT: D 774 GLN cc_start: 0.9392 (mp10) cc_final: 0.8870 (mp10) REVERT: D 788 MET cc_start: 0.9169 (mtm) cc_final: 0.8892 (mtm) REVERT: D 792 GLU cc_start: 0.9343 (tm-30) cc_final: 0.9132 (tm-30) REVERT: A 39 GLU cc_start: 0.9449 (mt-10) cc_final: 0.8975 (mp0) REVERT: A 66 THR cc_start: 0.8219 (p) cc_final: 0.7976 (p) REVERT: A 128 TYR cc_start: 0.8603 (m-10) cc_final: 0.8336 (m-10) REVERT: A 131 LYS cc_start: 0.9063 (mptt) cc_final: 0.8086 (tmmt) REVERT: A 140 THR cc_start: 0.9364 (p) cc_final: 0.9016 (t) REVERT: A 146 HIS cc_start: 0.9061 (m-70) cc_final: 0.8787 (m-70) REVERT: A 147 GLN cc_start: 0.9184 (mt0) cc_final: 0.8982 (mp10) REVERT: A 172 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7064 (mp0) REVERT: A 183 LEU cc_start: 0.8808 (mm) cc_final: 0.8562 (tp) REVERT: A 197 PHE cc_start: 0.7410 (m-80) cc_final: 0.7081 (m-80) REVERT: A 225 GLU cc_start: 0.7783 (tt0) cc_final: 0.7450 (pm20) REVERT: A 232 TYR cc_start: 0.8932 (m-80) cc_final: 0.8492 (m-80) REVERT: A 326 MET cc_start: 0.9083 (tmm) cc_final: 0.8635 (ptt) REVERT: A 345 ASP cc_start: 0.8806 (m-30) cc_final: 0.8527 (t70) REVERT: A 358 ASN cc_start: 0.9521 (m-40) cc_final: 0.9263 (m110) REVERT: A 477 HIS cc_start: 0.8563 (t-90) cc_final: 0.8308 (t-90) REVERT: A 533 PHE cc_start: 0.7549 (m-80) cc_final: 0.6505 (m-80) REVERT: A 534 LYS cc_start: 0.8852 (mppt) cc_final: 0.8602 (ptmt) REVERT: A 539 THR cc_start: 0.8915 (p) cc_final: 0.8583 (p) REVERT: A 611 TRP cc_start: 0.8058 (m100) cc_final: 0.7567 (m100) REVERT: A 663 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8298 (ptt-90) REVERT: A 698 GLU cc_start: 0.9353 (tm-30) cc_final: 0.9144 (tm-30) REVERT: A 707 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8247 (mp0) REVERT: A 736 LEU cc_start: 0.8567 (tp) cc_final: 0.8344 (tp) REVERT: A 737 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8650 (mm-30) REVERT: B 80 LYS cc_start: 0.9063 (mttt) cc_final: 0.8786 (ptpp) REVERT: B 100 PHE cc_start: 0.9185 (m-80) cc_final: 0.8921 (m-80) REVERT: B 102 ASP cc_start: 0.9063 (m-30) cc_final: 0.8771 (t70) REVERT: B 133 MET cc_start: 0.9192 (mmp) cc_final: 0.8896 (mpp) REVERT: B 134 ILE cc_start: 0.7647 (mt) cc_final: 0.7436 (mm) REVERT: B 135 MET cc_start: 0.8071 (mmp) cc_final: 0.7734 (mmp) REVERT: B 167 TRP cc_start: 0.8028 (m100) cc_final: 0.7374 (m100) REVERT: B 169 VAL cc_start: 0.8849 (t) cc_final: 0.8645 (p) REVERT: B 231 CYS cc_start: 0.6179 (p) cc_final: 0.5284 (p) REVERT: B 235 GLU cc_start: 0.8647 (tt0) cc_final: 0.8174 (tt0) REVERT: B 260 LEU cc_start: 0.9143 (pt) cc_final: 0.8805 (tp) REVERT: B 264 ASN cc_start: 0.9283 (m-40) cc_final: 0.8944 (p0) REVERT: B 267 LEU cc_start: 0.8987 (mp) cc_final: 0.7567 (mp) REVERT: B 293 ARG cc_start: 0.9480 (mtt180) cc_final: 0.9163 (mmm-85) REVERT: B 334 LEU cc_start: 0.9459 (mt) cc_final: 0.9210 (mm) REVERT: B 338 MET cc_start: 0.8638 (mmp) cc_final: 0.8212 (mmm) REVERT: B 385 LEU cc_start: 0.8802 (mm) cc_final: 0.8513 (mm) REVERT: B 437 ARG cc_start: 0.5257 (mtt180) cc_final: 0.3158 (mtt180) REVERT: B 473 PHE cc_start: 0.8381 (m-80) cc_final: 0.7873 (m-80) REVERT: B 496 MET cc_start: 0.8550 (mmm) cc_final: 0.7791 (mmm) REVERT: B 499 GLU cc_start: 0.9142 (tp30) cc_final: 0.8853 (tp30) REVERT: B 504 ARG cc_start: 0.9064 (mtt180) cc_final: 0.8449 (mmt90) REVERT: B 696 ASN cc_start: 0.8614 (m-40) cc_final: 0.8255 (m110) REVERT: B 705 MET cc_start: 0.9083 (tpp) cc_final: 0.8872 (mmm) REVERT: B 759 THR cc_start: 0.4213 (p) cc_final: 0.3462 (p) REVERT: B 781 GLN cc_start: 0.8510 (tp-100) cc_final: 0.8261 (tp-100) REVERT: B 787 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9149 (mp0) REVERT: B 790 GLU cc_start: 0.9116 (tp30) cc_final: 0.8570 (tp30) REVERT: B 792 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8892 (mt-10) REVERT: B 794 LEU cc_start: 0.8778 (mt) cc_final: 0.8004 (mt) REVERT: C 37 LYS cc_start: 0.9210 (ptpp) cc_final: 0.8980 (ptmm) REVERT: C 70 ASN cc_start: 0.9204 (p0) cc_final: 0.8996 (p0) REVERT: C 127 ILE cc_start: 0.9482 (mt) cc_final: 0.9216 (tp) REVERT: C 147 GLN cc_start: 0.9437 (mt0) cc_final: 0.9169 (mt0) REVERT: C 166 LEU cc_start: 0.9336 (mt) cc_final: 0.8982 (mt) REVERT: C 171 HIS cc_start: 0.8677 (t-90) cc_final: 0.7973 (t-90) REVERT: C 177 GLN cc_start: 0.8819 (tp40) cc_final: 0.8573 (tp-100) REVERT: C 181 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9205 (mt-10) REVERT: C 184 LEU cc_start: 0.9589 (mm) cc_final: 0.9261 (tp) REVERT: C 303 ASP cc_start: 0.9107 (m-30) cc_final: 0.8451 (t0) REVERT: C 306 ARG cc_start: 0.9167 (mtt180) cc_final: 0.8811 (mtt-85) REVERT: C 316 LYS cc_start: 0.9486 (tptp) cc_final: 0.9151 (tppt) REVERT: C 378 LYS cc_start: 0.8749 (mttt) cc_final: 0.8533 (tptp) REVERT: C 390 ARG cc_start: 0.8855 (mtt180) cc_final: 0.8145 (ptp90) REVERT: C 397 ARG cc_start: 0.9577 (mtt180) cc_final: 0.9153 (ttm-80) REVERT: C 400 ILE cc_start: 0.7857 (mt) cc_final: 0.7530 (mt) REVERT: C 405 GLN cc_start: 0.9566 (tp-100) cc_final: 0.9106 (tm-30) REVERT: C 477 HIS cc_start: 0.8976 (m90) cc_final: 0.8568 (m90) REVERT: C 536 GLN cc_start: 0.8535 (tp-100) cc_final: 0.8273 (tp-100) REVERT: C 539 THR cc_start: 0.9429 (m) cc_final: 0.9097 (p) REVERT: C 607 MET cc_start: 0.9169 (tmm) cc_final: 0.8892 (tmm) REVERT: C 634 MET cc_start: 0.8283 (ptt) cc_final: 0.7789 (ptt) REVERT: C 641 MET cc_start: 0.9414 (tmm) cc_final: 0.9096 (ttm) REVERT: C 696 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8110 (mt0) REVERT: C 697 VAL cc_start: 0.8438 (t) cc_final: 0.7153 (t) REVERT: C 736 LEU cc_start: 0.9049 (mt) cc_final: 0.8753 (mt) outliers start: 1 outliers final: 1 residues processed: 659 average time/residue: 0.3340 time to fit residues: 347.8234 Evaluate side-chains 557 residues out of total 2682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 556 time to evaluate : 2.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 67 optimal weight: 0.0470 chunk 243 optimal weight: 0.0050 chunk 101 optimal weight: 30.0000 chunk 249 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 overall best weight: 2.2098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 HIS D 515 ASN ** D 702 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 727 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 HIS ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 520 ASN ** C 780 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.108524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.081896 restraints weight = 172449.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.086076 restraints weight = 93802.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.089138 restraints weight = 61156.890| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.8809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24442 Z= 0.194 Angle : 0.715 14.982 33132 Z= 0.373 Chirality : 0.049 0.253 3790 Planarity : 0.004 0.048 4182 Dihedral : 5.998 30.467 3280 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.50 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.15), residues: 3028 helix: 0.02 (0.15), residues: 1226 sheet: -1.03 (0.28), residues: 328 loop : -1.87 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP C 636 HIS 0.016 0.001 HIS C 780 PHE 0.030 0.002 PHE A 639 TYR 0.021 0.002 TYR A 232 ARG 0.009 0.001 ARG D 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6765.62 seconds wall clock time: 121 minutes 26.91 seconds (7286.91 seconds total)